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Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

License: GNU General Public License v3.0

Python 100.00%

assembly genome-skimming-data fastg mitogenome chloroplast mitochondria plastome its ribosomal

getorganelle's Issues

A bug of GetOrganelle 1.6.2 when running in Python2.*

Hi @Kinggerm ,
I was trying to assembly the mitochondrial genome (plant) with this configuration:

GetOrganelle v1.6.2
Python 2.7.6 (default, Nov 13 2018, 12:45:42) [GCC 4.8.4]
Python libs: numpy 1.14.5; sympy 1.4; scipy 1.1.0
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30

This is the code:

.../install/bin/GetOrganelle/get_organelle_from_reads.py -1 P9104_1_sample_10G.fastq -2 P9104_2_sample_10G.fastq -o CP9104_mit_3 -R 50 -k 21,45,65,85,105 -P 100000 -F embplant_mt

However, I get this error:

2020-02-10 14:00:04,906 - INFO: Pre-reading fastq ...
2020-02-10 14:00:04,906 - INFO: Estimating reads to use ...
2020-02-10 14:00:05,657 - INFO: Tasting 100000+100000 reads ...
2020-02-10 14:00:12,638 - ERROR:
Traceback (most recent call last):
File "/home/oscarperez/install/bin/GetOrganelle/get_organelle_from_reads.py", line 3541, in main
random_seed=options.random_seed, verbose_log=options.verbose_log, log_handler=log_handler)
File "/home/oscarperez/install/bin/GetOrganelle/get_organelle_from_reads.py", line 997, in estimate_maximum_n_reads_using_mapping
log_handler=log_handler if verbose_log else None, verbose_log=verbose_log)
File "/home/oscarperez/install/bin/GetOrganelle/get_organelle_from_reads.py", line 1227, in pre_assembly_mapped_reads_for_base_cov
theses_words, original_fq_files, word_size=gathering_word_size, output=more_fq_file)
File "/home/oscarperez/install/bin/GetOrganelle/get_organelle_from_reads.py", line 1127, in extend_with_constant_words
seq_line = fq_f_input_handler.readline()
ValueError: Mixing iteration and read methods would lose data

Total cost 7.96 s

I'm not sure what the problem could be. I have successfully assembled the chloroplast genome from the same data set (45G).

Thanks in advance!

Resolving repetitive(?) region in animal mitochondrion

Hello!

I am assembling a beetle mitochondrial genome, using this mt genome from the same beetle family as the seed. It appears mostly assembled, except for one region that has many small repeats or fragments.
I'm wondering if you have any suggestions to obtain a circular assembly. I've tried playing around a bit with -w and --reduce-reads-for-coverage, with no better results.

Log: get_org.log.txt

Thanks very much!

GetOrganelle can't find dependencies

Hi @Kinggerm

when running GetOrganelle, I get the following warning:

WARNING: bowtie2 not in the path!

I get the same message for the other dependencies. However, all dependencies are in my $PATH and I can call them from the command line directly.

Do you have any idea what causes this?

Best,

Niklas

Error: Too few seed reads found!

Dear Jianjun Jin,

What should I do if I get this error: "Too few seed reads found"?
How do I change the -s parameter?
I've tried the --max-reads parameter, but my files are of 387,936 reads after trimming and filtering and I got the same error after setting the --max-reads parameter.

Here's the log I got:

GetOrganelle v1.7.0

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.8.5 | packaged by conda-forge | (default, Jul 22 2020, 17:10:02) [Clang 10.0.0 ]
PYTHON LIBS: GetOrganelleLib 1.7.0; numpy 1.19.0; sympy 1.6.1; scipy 1.5.1
DEPENDENCIES: Bowtie2 2.4.1; SPAdes 3.12.0; Blast 2.6.0
SEED DB: animal_mt 0.0.0
LABEL DB: animal_mt 0.0.0
WORKING DIR: /Users/getorganelle_doryctinae/CNIN4288
/opt/anaconda2/envs/getorganelle/bin/get_organelle_from_reads.py -1 CNIN4288_READ1.fq.gz -2 CNIN4288_READ2.fq.gz -o mtgenome_results -R 10 -k 21,45,65,85,105 -F animal_mt

2020-09-09 00:28:56,741 - INFO: Pre-reading fastq ...
2020-09-09 00:28:56,742 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-09-09 00:28:56,841 - INFO: Tasting 100000+100000 reads ...
2020-09-09 00:34:22,015 - INFO: Estimating reads to use finished.
2020-09-09 00:34:22,025 - INFO: Unzipping reads file: CNIN4288_READ1.fq.gz (29259677 bytes)
2020-09-09 00:34:22,606 - INFO: Unzipping reads file: CNIN4288_READ2.fq.gz (30627486 bytes)
2020-09-09 00:34:23,278 - INFO: Counting read qualities ...
2020-09-09 00:34:23,415 - INFO: Identified quality encoding format = Illumina 1.8+
2020-09-09 00:34:23,418 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2020-09-09 00:34:23,462 - INFO: Mean error rate = 0.002
2020-09-09 00:34:23,463 - INFO: Counting read lengths ...
2020-09-09 00:34:24,483 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2020-09-09 00:34:24,483 - INFO: Reads used = 387936+387936
2020-09-09 00:34:24,483 - INFO: Pre-reading fastq finished.

2020-09-09 00:34:24,483 - INFO: Making seed reads ...
2020-09-09 00:34:24,485 - INFO: Seed bowtie2 index existed!
2020-09-09 00:34:24,485 - INFO: Mapping reads to seed bowtie2 index ...
2020-09-09 00:34:42,693 - INFO: Mapping finished.
2020-09-09 00:34:42,693 - INFO: Seed reads made: mtgenome_results/seed/animal_mt.initial.fq (9223 bytes)
2020-09-09 00:34:42,694 - ERROR: Too few seed reads found! Please change your seed file (-s) or increase your data input (--max-reads/--reduce-reads-for-coverage)!
2020-09-09 00:34:42,694 - ERROR:
Traceback (most recent call last):
File "/opt/anaconda2/envs/getorganelle/bin/get_organelle_from_reads.py", line 3797, in main
seed_fq, seed_sam, new_seed_f = making_seed_reads_using_mapping(
File "/opt/anaconda2/envs/getorganelle/bin/get_organelle_from_reads.py", line 2931, in making_seed_reads_using_mapping
exit()
File "/opt/anaconda2/envs/getorganelle/lib/python3.8/_sitebuiltins.py", line 26, in call
raise SystemExit(code)
SystemExit: None

Total cost 347.66 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

Thanks in advance for your help!

Ruben.

MemoryError

Hello,
I am doing the plant mitochondrial genome assembly with the following commands. But I am getting a MemoryError issue. The same parameter has used for another mitochondrial genome assembly.

get_organelle_from_reads.py -1forward_paired.fq.gz -2 reverse_paired.fq.gz -o get_organelle/ -R 50 -P 1000000 -F embplant_mt --memory-save -w 95 --reduce-reads-for-coverage inf

log.txt

2020-11-18 09:37:23,901 - INFO: Counting read qualities ...
2020-11-18 09:37:24,110 - INFO: Identified quality encoding format = Illumina 1.8+
2020-11-18 09:37:24,111 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2020-11-18 09:37:24,175 - INFO: Mean error rate = 0.0146
2020-11-18 09:37:24,176 - INFO: Counting read lengths ...
2020-11-18 09:41:21,922 - INFO: Mean = 151.0 bp, maximum = 151 bp.
2020-11-18 09:41:21,922 - INFO: Reads used = 72894963+72894963
2020-11-18 09:41:21,922 - INFO: Pre-reading fastq finished.

2020-11-18 09:41:21,922 - INFO: Making seed reads ...
2020-11-18 09:41:21,952 - INFO: Seed bowtie2 index existed!
2020-11-18 09:41:21,952 - INFO: Mapping reads to seed bowtie2 index ...
2020-11-18 10:14:08,892 - INFO: Mapping finished.
2020-11-18 10:14:08,893 - INFO: Seed reads made: ./../../raman/cma_mt/get_organelle/seed/embplant_mt.initial.fq (13572326 bytes)
2020-11-18 10:14:08,916 - INFO: Making seed reads finished.

2020-11-18 10:14:08,916 - INFO: Checking seed reads and parameters ...
2020-11-18 10:14:11,177 - INFO: Estimated embplant_mt-hitting base-coverage = 133.73
2020-11-18 10:14:11,665 - INFO: Setting '--max-extending-len inf'
2020-11-18 10:14:11,725 - INFO: Checking seed reads and parameters finished.

2020-11-18 10:14:11,725 - INFO: Making read index ...
2020-11-18 10:35:14,221 - INFO: Mem 19.971 G, 145789926 reads
2020-11-18 10:35:23,848 - INFO: Making read index finished.

2020-11-18 10:35:23,849 - INFO: Extending ...
2020-11-18 10:35:23,849 - INFO: Adding initial words ...
2020-11-18 10:35:25,549 - INFO: AW 1414726
2020-11-18 10:56:53,068 - INFO: Round 1: 145789926/145789926 AI 2547987 AW 20138238 Mem 4.131
2020-11-18 11:18:14,011 - INFO: Round 2: 145789926/145789926 AI 4002492 AW 29878554 Mem 5.502
2020-11-18 11:39:52,946 - INFO: Round 3: 145789926/145789926 AI 4844430 AW 49387612 Mem 9.185
2020-11-18 12:02:22,295 - INFO: Round 4: 145789926/145789926 AI 6248245 AW 85261724 Mem 16.365
2020-11-18 12:18:09,770 - ERROR: ound 5: 79960513/145789926 AI 8101461 AW 131499852
Traceback (most recent call last):
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 3879, in main
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 2371, in extending_no_lim
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 2217, in
File "/home/raman/anaconda3/lib/python3.7/codecs.py", line 322, in decode
MemoryError
--- Logging error ---
Traceback (most recent call last):
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 3879, in main
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 2371, in extending_no_lim
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 2217, in
File "/home/raman/anaconda3/lib/python3.7/codecs.py", line 322, in decode
MemoryError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/raman/anaconda3/lib/python3.7/logging/init.py", line 1025, in emit
File "/home/raman/anaconda3/lib/python3.7/logging/init.py", line 869, in format
File "/home/raman/anaconda3/lib/python3.7/logging/init.py", line 610, in format
File "/home/raman/anaconda3/lib/python3.7/logging/init.py", line 550, in formatTime
MemoryError
Call stack:
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 4045, in
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 4036, in main
Message: ''
Arguments: ()
Traceback (most recent call last):
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 3879, in main
echo_step=echo_step, log_handler=log_handler)
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 2371, in extending_no_lim
this_c_seq = next(reads_generator)
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 2217, in
reads_generator = (this_read.strip() for this_read in
File "/home/raman/anaconda3/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
MemoryError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 4045, in
main()
File "/home/raman/anaconda3/bin/get_organelle_from_reads.py", line 4037, in main
log_handler = simple_log(log_handler, out_base, prefix=options.prefix + "get_org.")
File "/home/raman/anaconda3/lib/python3.7/site-packages/GetOrganelleLib/pipe_control_func.py", line 69, in simple_log
logfile = logging.FileHandler(os.path.join(output_base, prefix + 'log.txt'), mode='a')
File "/home/raman/anaconda3/lib/python3.7/logging/init.py", line 1087, in init
StreamHandler.init(self, self._open())
File "/home/raman/anaconda3/lib/python3.7/logging/init.py", line 1116, in _open
return open(self.baseFilename, self.mode, encoding=self.encoding)
MemoryError

Problem running

Good day,

I am having trouble running GetOrganelle on our cluster.

My command for running GetOrganelle:

singularity exec /tools/containers/getorganelle/getorganelle-test-1.simg get_organelle_reads.py -1 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R1.fastq -2 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R2.fastq -o /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5 -R 15 -k 45,65,85,105 -F plant_cp

The log file:

GetOrganelle v1.5.1c

gets organelle reads and genomes from genome skimming data by extending.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.1 (default, Dec 14 2018, 19:28:38)
[GCC 7.3.0]
/GetOrganelle/get_organelle_reads.py -1 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R1.fastq -2 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R2.fastq -o /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5 -R 15 -k 45,65,85,105 -F plant_cp

2019-03-25 15:02:59,898 - INFO: Pre-reading fastq ...
2019-03-25 15:02:59,899 - INFO: Counting read qualities ...
2019-03-25 15:03:23,316 - INFO: Number of reads exceeded 15000000 in L5_R1.fastq, only top 15000000 reads are used in downstream analysis.
2019-03-25 15:03:46,312 - INFO: Number of reads exceeded 15000000 in L5_R2.fastq, only top 15000000 reads are used in downstream analysis.
2019-03-25 15:04:04,830 - INFO: Identified quality encoding format = Sanger
2019-03-25 15:04:05,080 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2019-03-25 15:04:15,128 - INFO: Mean error rate = 0.0019
2019-03-25 15:04:15,267 - INFO: Counting read lengths ...
2019-03-25 15:05:06,647 - INFO: Mean = 119.9 bp, maximum = 125 bp.
2019-03-25 15:05:06,647 - INFO: Reads used = 30000000
2019-03-25 15:05:06,647 - INFO: Pre-reading fastq finished.

2019-03-25 15:05:06,647 - INFO: Making seed reads ...
2019-03-25 15:05:06,653 - INFO: Making seed - bowtie2 index ...
2019-03-25 15:05:06,729 - ERROR:
Settings:
 Output files: "/GetOrganelle/Library/SeqReference/plant_cp.fasta.index.*.bt2l"
 Line rate: 7 (line is 128 bytes)
 Lines per side: 1 (side is 128 bytes)
 Offset rate: 4 (one in 16)
 FTable chars: 10
 Strings: unpacked
 Max bucket size: default
 Max bucket size, sqrt multiplier: default
 Max bucket size, len divisor: 4
 Difference-cover sample period: 1024
 Endianness: little
 Actual local endianness: little
 Sanity checking: disabled
 Assertions: disabled
 Random seed: 0
 Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
 /GetOrganelle/Library/SeqReference/plant_cp.fasta
Building a LARGE index
Reading reference sizes
Could not open index file for writing: "/GetOrganelle/Library/SeqReference/plant_cp.fasta.index.3.bt2l"
Please make sure the directory exists and that permissions allow writing by
Bowtie.
 Time reading reference sizes: 00:00:00
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: /opt/miniconda/bin/bowtie2-build-l --wrapper basic-0 /GetOrganelle/Library/SeqReference/plant_cp.fasta /GetOrganelle/Library/SeqReference/plant_cp.fasta.index
Deleting "/GetOrganelle/Library/SeqReference/plant_cp.fasta.index.3.bt2l" file written during aborted indexing attempt.
Deleting "/GetOrganelle/Library/SeqReference/plant_cp.fasta.index.4.bt2l" file written during aborted indexing attempt.

2019-03-25 15:05:06,730 - ERROR:
Traceback (most recent call last):
 File "/GetOrganelle/get_organelle_reads.py", line 2557, in main
   log=log)
 File "/GetOrganelle/get_organelle_reads.py", line 1846, in mapping_with_bowtie2
   exit()
 File "/opt/miniconda/lib/python3.7/_sitebuiltins.py", line 26, in __call__
   raise SystemExit(code)
SystemExit: None

Total cost 127.85 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

Any idea as to what is happening, or how I can fix it?

Kind regards,
Allison

ERROR: Slimming mtgenome_results/filtered_spades/K45/assembly_graph.fastg failed

Dear Jianjun Jin,

Hi! It's me again, Rubén.

I was running a sample in GO and got these messages:
"2020-09-26 14:55:33,237 - ERROR: Slimming mtgenome_results/filtered_spades/K65/assembly_graph.fastg failed.
2020-09-26 14:55:34,165 - ERROR: Slimming mtgenome_results/filtered_spades/K45/assembly_graph.fastg failed."

What should I do to fix this problem?
Here's the log I got:

GetOrganelle v1.7.0

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.8.5 | packaged by conda-forge | (default, Jul 22 2020, 17:10:02) [Clang 10.0.0 ]
PYTHON LIBS: GetOrganelleLib 1.7.0; numpy 1.19.0; sympy 1.6.1; scipy 1.5.1
DEPENDENCIES: Bowtie2 2.4.1; SPAdes 3.12.0; Blast 2.6.0
SEED DB: animal_mt 0.0.0
LABEL DB: animal_mt 0.0.0
WORKING DIR: /Users/alejandrozaldivar/getorganelle_doryctinae/BBP552
/opt/anaconda2/envs/getorganelle/bin/get_organelle_from_reads.py -1 BBP552_READ1.fastq.gz -2 BBP552_READ2.fastq.gz -o mtgenome_results -R 15 -k 21,45,65,85,105 -F animal_mt

2020-09-26 14:50:15,605 - INFO: Pre-reading fastq ...
2020-09-26 14:50:15,606 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-09-26 14:50:15,696 - INFO: Tasting 100000+100000 reads ...
2020-09-26 14:52:54,699 - INFO: Tasting 500000+500000 reads ...
2020-09-26 14:53:29,366 - INFO: Estimating reads to use finished.
2020-09-26 14:53:29,367 - INFO: Unzipping reads file: BBP552_READ1.fastq.gz (113972404 bytes)
2020-09-26 14:53:31,074 - INFO: Unzipping reads file: BBP552_READ2.fastq.gz (114963105 bytes)
2020-09-26 14:53:33,021 - INFO: Counting read qualities ...
2020-09-26 14:53:33,134 - INFO: Identified quality encoding format = Sanger
2020-09-26 14:53:33,135 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2020-09-26 14:53:33,189 - INFO: Mean error rate = 0.0026
2020-09-26 14:53:33,191 - INFO: Counting read lengths ...
2020-09-26 14:53:36,376 - INFO: Mean = 118.6 bp, maximum = 125 bp.
2020-09-26 14:53:36,376 - INFO: Reads used = 1276687+1276687
2020-09-26 14:53:36,376 - INFO: Pre-reading fastq finished.

2020-09-26 14:53:36,376 - INFO: Making seed reads ...
2020-09-26 14:53:36,376 - INFO: Seed bowtie2 index existed!
2020-09-26 14:53:36,376 - INFO: Mapping reads to seed bowtie2 index ...
2020-09-26 14:54:24,324 - INFO: Mapping finished.
2020-09-26 14:54:24,324 - INFO: Seed reads made: mtgenome_results/seed/animal_mt.initial.fq (70772 bytes)
2020-09-26 14:54:24,324 - INFO: Making seed reads finished.

2020-09-26 14:54:24,324 - INFO: Checking seed reads and parameters ...
2020-09-26 14:54:24,324 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2020-09-26 14:54:24,325 - INFO: If the result graph is not a circular organelle genome,
2020-09-26 14:54:24,325 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2020-09-26 14:54:26,488 - INFO: Pre-assembling mapped reads ...
2020-09-26 14:54:28,103 - ERROR: slimming the pre-assembled graph failed.
2020-09-26 14:54:28,108 - INFO: Pre-assembling mapped reads finished.
2020-09-26 14:54:28,108 - INFO: Estimated animal_mt-hitting base-coverage = 61.20
2020-09-26 14:54:28,250 - INFO: Estimated word size(s): 78
2020-09-26 14:54:28,250 - INFO: Setting '-w 78'
2020-09-26 14:54:28,250 - INFO: Setting '--max-extending-len inf'
2020-09-26 14:54:28,320 - INFO: Checking seed reads and parameters finished.

2020-09-26 14:54:28,320 - INFO: Making read index ...
2020-09-26 14:54:45,147 - INFO: 2020940 candidates in all 2553374 reads
2020-09-26 14:54:45,151 - INFO: Pre-grouping reads ...
2020-09-26 14:54:45,151 - INFO: Setting '--pre-w 78'
2020-09-26 14:54:45,403 - INFO: 200000/328283 used/duplicated
2020-09-26 14:54:58,502 - INFO: 9867 groups made.
2020-09-26 14:54:58,673 - INFO: Making read index finished.

2020-09-26 14:54:58,673 - INFO: Extending ...
2020-09-26 14:54:58,673 - INFO: Adding initial words ...
2020-09-26 14:54:58,677 - INFO: AW 2958
2020-09-26 14:55:07,803 - INFO: Round 1: 2020940/2020940 AI 50 AW 3288
2020-09-26 14:55:16,754 - INFO: Round 2: 2020940/2020940 AI 51 AW 3330
2020-09-26 14:55:25,741 - INFO: Round 3: 2020940/2020940 AI 51 AW 3330
2020-09-26 14:55:25,741 - INFO: No more reads found and terminated ...
2020-09-26 14:55:29,470 - INFO: Extending finished.

2020-09-26 14:55:29,512 - INFO: Separating filtered fastq file ...
2020-09-26 14:55:29,513 - INFO: Setting '-k 21,45,65,85,105'
2020-09-26 14:55:29,514 - INFO: Assembling using SPAdes ...
2020-09-26 14:55:29,531 - INFO: spades.py -t 1 -1 mtgenome_results/filtered_1_paired.fq -2 mtgenome_results/filtered_2_paired.fq --s1 mtgenome_results/filtered_1_unpaired.fq --s2 mtgenome_results/filtered_2_unpaired.fq -k 21,45,65,85,105 -o mtgenome_results/filtered_spades
2020-09-26 14:55:31,890 - WARNING: SPAdes failed for '-k 85'!
2020-09-26 14:55:31,891 - WARNING: If you need result based on kmer=85 urgently, please check mtgenome_results/filtered_spades/spades.log
2020-09-26 14:55:31,891 - WARNING: GetOrganelle would continue to process results based on kmer=21,45,65.
2020-09-26 14:55:31,891 - INFO: Assembling finished with warnings.

2020-09-26 14:55:33,237 - ERROR: Slimming mtgenome_results/filtered_spades/K65/assembly_graph.fastg failed.
2020-09-26 14:55:34,165 - ERROR: Slimming mtgenome_results/filtered_spades/K45/assembly_graph.fastg failed.

Total cost 319.80 s
Thank you!

Thanks again for your help!

Rubén.

Stuck on slimming stage

I ran the analysis using the following setup:
get_organelle_from_reads.py -1 Fc_KEIB_AP00245_R1.fastq.gz -2 Fc_KEIB_AP00245_R2.fastq.gz -t 8 -o Ferula_no_custom_seed_w100_maxreads150_coverage500_maxwords6E8_seedDaucus.plastome -F embplant_pt -R 10 -w 100 --max-reads 150000000 --max-n-words=6E8 -s ./Daucus_carota_cpDNA.fasta

Everything went smooth till the slimming where the program was stuck by several days. I killed the analysis and reran it. However, I met the same problem. I have no idea what is wrong.

Best
Marcin

Spontaneous error with python "index out of range"

Hi, @Kinggerm,

I am trying to use GetOrganelle to assemble both the chloroplast and the mitochondrion of my plant. In the process I have been facing an "index out of range error" from python (that goes to stderr):

Traceback (most recent call last):
  File "/home/svillanu/Programs/GetOrganelle/get_organelle_from_reads.py", line 3502, in <module>
    main()
  File "/home/svillanu/Programs/GetOrganelle/get_organelle_from_reads.py", line 3142, in main
    options, log_handler, previous_attributes = get_options(description=title, version=get_versions())
  File "/home/svillanu/Programs/GetOrganelle/get_organelle_from_reads.py", line 570, in get_options
    dep_versions_info.append("Blast " + this_lines[1].strip().split()[2].replace(",", "").strip())
IndexError: list index out of range

In the beginning, I managed to get chloroplast running, and this error just appeared when I tried to assemble the mitochondrion. But as that process failed, and I resubmitted I'm getting the same error with the chloroplast as well (without changing anything). The following is one example of this problem. The log is not very informative though:

Log:

GetOrganelle v1.6.1a

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56)  [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Python libs: numpy 1.16.4; sympy 1.4; scipy 1.3.0

GetOrganelle v1.6.1a

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.6.5 | packaged by conda-forge | (default, Apr  6 2018, 13:39:56)  [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Python libs: numpy 1.16.4; sympy 1.4; scipy 1.3.0

Here is the command line that produces it:

get_organelle_from_reads.py -1 $pe1 -2 $pe2 -o $output -F embplant_pt -t $threads -k 21,45,65,85,105 --max-reads=10E7 --which-blast $blast --which-bandage $bandage

Where:

threads=$SLURM_CPUS_PER_TASK   ## 16 
folder=$(pwd)
pe1="$folder/reads/WGS_pe1.fastq"
pe2="$folder/reads/WGS_pe2.fastq"
output="$folder/output"
blast="/home/svillanu/Programs/GetOrganelle/GetOrganelleDep/linux/ncbi-blast"
bandage="/home/svillanu/.conda/envs/Spades/bin"

Something that I find curious, is that at the beginning, as aforementioned, the chloroplast process was running ok, but the mitochondrion presented this error; Even though it is exactly the same configuration (same data and parameters), it only changes the -F option to embplant_mt.

Do you have any idea of what could be happening here?
Thanks in advance!

conda install problem

The command and failure message are following:
$conda install -c bioconda getorganelle
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve.Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
Examining widgetsnbextension:

After updating conda the issue also happen.

Any reply will be welcomed.

Change in parameters to try get circular genome

Good day,

I would like your input on how I can gain better results from GetOrganelle.

The output file:

GetOrganelle v1.5.1c

gets organelle reads and genomes from genome skimming data by extending.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.1 (default, Dec 14 2018, 19:28:38) 
[GCC 7.3.0]
/GetOrganelle/get_organelle_reads.py -1 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R1.fastq -2 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R2.fastq -o /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5 -R 15 -k 21,35,55,65,85,105,115 -F plant_cp -s /usr/people/astander/GetOrganelle/Library/SeqReference/plant_cp.fasta


GetOrganelle v1.5.1c

gets organelle reads and genomes from genome skimming data by extending.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.1 (default, Dec 14 2018, 19:28:38) 
[GCC 7.3.0]
/GetOrganelle/get_organelle_reads.py -1 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R1.fastq -2 /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R2.fastq -o /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5 -R 15 -k 21,35,55,65,85,105,115 -F plant_cp -s /usr/people/astander/GetOrganelle/Library/SeqReference/plant_cp.fasta

2019-03-28 18:32:21,310 - INFO: Pre-reading fastq ...
2019-03-28 18:32:21,310 - INFO: Counting read qualities ...
2019-03-28 18:34:22,105 - INFO: Number of reads exceeded 15000000 in L5_R1.fastq, only top 15000000 reads are used in downstream analysis.
2019-03-28 18:36:15,704 - INFO: Number of reads exceeded 15000000 in L5_R2.fastq, only top 15000000 reads are used in downstream analysis.
2019-03-28 18:36:43,662 - INFO: Identified quality encoding format = Sanger
2019-03-28 18:36:44,037 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2019-03-28 18:36:52,971 - INFO: Mean error rate = 0.0019
2019-03-28 18:36:53,306 - INFO: Counting read lengths ...
2019-03-28 18:38:10,228 - INFO: Mean = 119.9 bp, maximum = 125 bp.
2019-03-28 18:38:10,228 - INFO: Reads used = 30000000
2019-03-28 18:38:10,228 - INFO: Pre-reading fastq finished.

2019-03-28 18:38:10,228 - INFO: Making seed reads ...
2019-03-28 18:38:11,698 - INFO: Making seed - bowtie2 index ...
2019-03-28 18:38:12,606 - INFO: Making seed - bowtie2 index finished.
2019-03-28 18:38:37,332 - INFO: Mapping reads to seed - bowtie2 index ...
2019-03-28 18:52:59,248 - INFO: Mapping finished.
2019-03-28 18:52:59,320 - INFO: Seed reads made: /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/Initial.mapped.fq (218.47 M)
2019-03-28 18:53:00,211 - INFO: Making seed reads finished.

2019-03-28 18:53:00,230 - INFO: Checking seed reads and parameters ...
2019-03-28 18:53:58,051 - INFO: Estimated plant_cp base-coverage = 1437.81
2019-03-28 18:53:58,058 - INFO: Setting '-w 89'
2019-03-28 18:53:58,104 - INFO: The automatically-estimated word size does not ensure the best choice.
2019-03-28 18:53:58,254 - INFO: If the result graph is not a circular organelle genome, 
2019-03-28 18:53:58,280 - INFO: you could adjust the word size for another new run.
2019-03-28 18:53:58,416 - INFO: Checking seed reads and parameters finished.

2019-03-28 18:53:58,459 - INFO: Making read index ...
2019-03-28 18:58:20,563 - WARNING: Number of reads exceeded 15000000 in /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R1.fastq, only top 15000000 reads are used in downstream analysis.
2019-03-28 19:02:44,799 - WARNING: Number of reads exceeded 15000000 in /usr/people/astander/00_GenomeRooibos/00_Data/00_RawData/L5_R2.fastq, only top 15000000 reads are used in downstream analysis.
2019-03-28 19:03:34,260 - INFO: 25550660 candidates in all 30000000 reads
2019-03-28 19:03:34,630 - INFO: Pre-grouping reads ...
2019-03-28 19:03:36,545 - INFO: Setting '--pre-w 89'
2019-03-28 19:03:44,259 - INFO: 200000/714935 used/duplicated
2019-03-28 19:04:21,710 - INFO: 8443 groups made.
2019-03-28 19:04:36,254 - INFO: Making read index finished.

2019-03-28 19:04:36,260 - INFO: Extending ...
2019-03-28 19:04:36,268 - INFO: Adding initial words ...
2019-03-28 19:05:12,583 - INFO: AW 2584834
2019-03-28 19:09:41,555 - INFO: Round 1: 25550660/25550660 AI 518395 AW 3904808
2019-03-28 19:13:54,598 - INFO: Round 2: 25550660/25550660 AI 531945 AW 4070496
2019-03-28 19:18:10,411 - INFO: Round 3: 25550660/25550660 AI 576194 AW 4626522
2019-03-28 19:22:25,169 - INFO: Round 4: 25550660/25550660 AI 663383 AW 5701564
2019-03-28 19:26:40,507 - INFO: Round 5: 25550660/25550660 AI 814082 AW 7563412
2019-03-28 19:31:15,998 - INFO: Round 6: 25550660/25550660 AI 1496646 AW 15215974
2019-03-28 19:35:43,556 - INFO: Round 7: 25550660/25550660 AI 1950207 AW 21505244
2019-03-28 19:39:58,525 - INFO: Round 8: 25550660/25550660 AI 2259693 AW 26012790
2019-03-28 19:44:18,409 - INFO: Round 9: 25550660/25550660 AI 2641614 AW 31061132
2019-03-28 19:48:40,035 - INFO: Round 10: 25550660/25550660 AI 2857690 AW 34449698
2019-03-28 19:53:05,617 - INFO: Round 11: 25550660/25550660 AI 2995090 AW 36733566
2019-03-28 19:57:21,129 - INFO: Round 12: 25550660/25550660 AI 3107392 AW 38560654
2019-03-28 20:01:38,964 - INFO: Round 13: 25550660/25550660 AI 3198826 AW 40018076
2019-03-28 20:06:01,309 - INFO: Round 14: 25550660/25550660 AI 3262681 AW 41055100
2019-03-28 20:10:18,452 - INFO: Round 15: 25550660/25550660 AI 3315775 AW 41891528
2019-03-28 20:10:18,476 - INFO: Hit the round limit 15 and terminated ...
2019-03-28 20:13:09,421 - INFO: Extending finished.

2019-03-28 20:13:09,452 - INFO: Separating filtered fastq file ... 
2019-03-28 20:13:52,634 - INFO: Separating filtered fastq file finished!
2019-03-28 20:13:52,771 - INFO: Setting '-k 21,35,55,65,85,105,115'
2019-03-28 20:13:53,043 - INFO: Assembling using SPAdes ...
2019-03-28 22:50:44,347 - INFO: Insert size = 258.122, deviation = 107.267, left quantile = 143, right quantile = 405
2019-03-28 22:50:44,373 - INFO: Assembling finished.

2019-03-28 22:50:44,374 - INFO: Slimming and disentangling graph ...
2019-03-28 22:50:50,990 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K115/assembly_graph.fastg finished!
2019-03-28 22:50:54,178 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K115/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:50:54,196 - INFO: Disentangling failed: Multiple isolated plant_cp components detected! Broken or contamination?
2019-03-28 22:50:57,694 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K105/assembly_graph.fastg finished!
2019-03-28 22:50:57,695 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K105/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:50:57,710 - INFO: Disentangling failed: Multiple isolated plant_cp components detected! Broken or contamination?
2019-03-28 22:51:00,271 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K85/assembly_graph.fastg finished!
2019-03-28 22:51:00,272 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K85/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:51:02,591 - INFO: Disentangling failed: Incomplete/Complicated graph: please check around EDGE_11713466_11330368_9962576_11958552!
2019-03-28 22:51:17,166 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K65/assembly_graph.fastg finished!
2019-03-28 22:51:17,167 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K65/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:51:18,353 - INFO: Disentangling failed: Incomplete/Complicated graph: please check around EDGE_14025358_14042764!
2019-03-28 22:51:35,009 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K55/assembly_graph.fastg finished!
2019-03-28 22:51:35,010 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K55/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:51:36,440 - WARNING: The graph might suffer from contamination or polymorphism!
2019-03-28 22:51:39,376 - INFO: Disentangling failed: Incomplete/Complicated graph: please check around EDGE_14651591_9465799_13808679_14535005!
2019-03-28 22:51:52,145 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K35/assembly_graph.fastg finished!
2019-03-28 22:51:52,146 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K35/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:53:26,696 - INFO: Disentangling failed: Multiple isolated plant_cp components detected! Broken or contamination?
2019-03-28 22:53:52,305 - INFO: Slimming      /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K21/assembly_graph.fastg finished!
2019-03-28 22:53:52,306 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K21/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as a circular genome ... 
2019-03-28 22:59:40,990 - INFO: Disentangling failed: Multiple isolated plant_cp components detected! Broken or contamination?
2019-03-28 22:59:41,113 - INFO: Disentangling /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/filtered_spades/K115/assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg as contig(s) ... 
2019-03-28 22:59:41,915 - INFO: Vertex_9097300 #copy = 4
2019-03-28 22:59:41,915 - INFO: Vertex_9111140 #copy = 2
2019-03-28 22:59:41,916 - INFO: Vertex_9152396 #copy = 1
2019-03-28 22:59:41,916 - INFO: Vertex_9157396 #copy = 2
2019-03-28 22:59:41,916 - INFO: Vertex_9157452 #copy = 1
2019-03-28 22:59:41,916 - INFO: Vertex_9157504 #copy = 2
2019-03-28 22:59:41,916 - INFO: Vertex_9157668 #copy = 1
2019-03-28 22:59:41,916 - INFO: Average plant_cp kmer-coverage = 93.45
2019-03-28 22:59:41,916 - INFO: Average plant_cp base-coverage = 1884.582
2019-03-28 22:59:41,916 - INFO: Slimming and disentangling graph finished!

2019-03-28 22:59:41,917 - INFO: Writing output ...
2019-03-28 22:59:41,924 - WARNING: Multiple repeat patterns appeared in your data, a more balanced pattern (always the repeat_pattern1) would be suggested for plastomes with inverted repeats!
2019-03-28 22:59:41,924 - WARNING: Multiple genome structures produced!
2019-03-28 22:59:41,924 - WARNING: Please check the existence of those isomers by using reads mapping (library information) or longer reads.
2019-03-28 22:59:41,930 - INFO: Writing PATH1 of plant_cp contig(s) to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.repeat_pattern1.1.path_sequence.fasta
2019-03-28 22:59:41,934 - INFO: Writing PATH2 of plant_cp contig(s) to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.repeat_pattern1.2.path_sequence.fasta
2019-03-28 22:59:41,938 - INFO: Writing PATH3 of plant_cp contig(s) to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.repeat_pattern2.3.path_sequence.fasta
2019-03-28 22:59:41,942 - INFO: Writing PATH4 of plant_cp contig(s) to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.repeat_pattern2.4.path_sequence.fasta
2019-03-28 22:59:41,946 - INFO: Writing PATH5 of plant_cp contig(s) to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.repeat_pattern2.5.path_sequence.fasta
2019-03-28 22:59:41,950 - INFO: Writing PATH6 of plant_cp contig(s) to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.repeat_pattern2.6.path_sequence.fasta
2019-03-28 22:59:41,950 - INFO: Writing GRAPH to /usr/people/astander/00_GenomeRooibos/06_Chloroplast/00_GetOrganelle/chloroplast_output_L5/plant_cp.K115.contigs.graph1.selected_graph.gfa
2019-03-28 22:59:41,952 - INFO: Result status: 2 contig(s)
2019-03-28 22:59:42,134 - INFO: Writing output finished.
2019-03-28 22:59:42,135 - INFO: Please ...
2019-03-28 22:59:42,135 - INFO: load the graph file 'assembly_graph.fastg.extend_plant_cp.del_plant_mt.fastg' in K115,K105,K85,K65,K55,K35,K21
2019-03-28 22:59:42,135 - INFO: load the CSV file 'assembly_graph.fastg.extend_plant_cp.del_plant_mt.csv' in K115,K105,K85,K65,K55,K35,K21
2019-03-28 22:59:42,135 - INFO: visualize and confirm the incomplete result in Bandage.
2019-03-28 22:59:42,135 - INFO: If the result is nearly complete, 
2019-03-28 22:59:42,135 - INFO: you can also adjust the arguments to try again.
2019-03-28 22:59:42,135 - INFO: If you have questions for us, please provide us with the get_org.log.txt file and the graph in the format you like!

Total cost 16043.11 s
Thank you!

The graph looks as follows:

I applied the changes you suggested via our email conversation.

What other changes should I first look at, to try get a circular genome?

Thank you for your time,

Kind regards,
Allison

Error in SPAdes

Operating System: ubuntu 18.04
Codes: get_organelle_from_reads.py -1 ../Cleandata/CSZ/CSZ_R1.fq -2 ../Cleandata/CSZ/CSZ_R2.fq -o cszmt --fast --memory-unlimited -F embplant_mt -t 144 --reduce-reads-for-coverage=300 --spades-options="-t 144 -m 1800"

Here is the get_org.log.txt
GetOrganelle v1.7.1

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.6 (default, Jan 8 2020, 19:59:22) [GCC 7.3.0]
PYTHON LIBS: GetOrganelleLib 1.7.1; numpy 1.18.5; sympy 1.6.1; scipy 1.4.1; psutil 5.7.0
DEPENDENCIES: Bowtie2 2.3.4.1; SPAdes 3.13.0; Blast 2.6.0
SEED DB: embplant_mt 0.0.0; embplant_pt 0.0.0
LABEL DB: embplant_mt 0.0.0; embplant_pt 0.0.0
WORKING DIR: /media/lst/ed8412ea-f84d-40b5-b433-1a157fbfbe7d/chenshuzhangmt/Cleandata/get
/home/lst/miniconda3/bin/get_organelle_from_reads.py -1 ../Cleandata/CSZ/CSZ_R1.fq -2 ../Cleandata/CSZ/CSZ_R2.fq -o cszmt --fast --memory-unlimited -F embplant_mt -t 144 --r
educe-reads-for-coverage=300 "--spades-options=-t 144 -m 1800"

2020-08-07 10:13:07,368 - INFO: Pre-reading fastq ...
2020-08-07 10:13:07,368 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-08-07 10:13:07,462 - INFO: Tasting 100000+100000 reads ...
2020-08-07 10:13:27,888 - INFO: Tasting 500000+500000 reads ...
2020-08-07 10:14:06,095 - INFO: Estimating reads to use finished.
2020-08-07 10:17:29,625 - INFO: Counting read qualities ...
2020-08-07 10:17:29,804 - INFO: Identified quality encoding format = Sanger
2020-08-07 10:17:29,844 - INFO: Mean error rate = 0.0024
2020-08-07 10:17:29,844 - INFO: Counting read lengths ...
2020-08-07 10:19:08,436 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2020-08-07 10:19:08,436 - INFO: Reads used = 39011704+39011704
2020-08-07 10:19:08,436 - INFO: Pre-reading fastq finished.

2020-08-07 10:19:08,436 - INFO: Making seed reads ...
2020-08-07 10:19:08,436 - INFO: Seed bowtie2 index existed!
2020-08-07 10:19:08,437 - INFO: Mapping reads to seed bowtie2 index ...
2020-08-07 10:33:19,444 - INFO: Mapping finished.
2020-08-07 10:33:19,444 - INFO: Seed reads made: cszmt/seed/embplant_mt.initial.fq (67910006 bytes)
2020-08-07 10:33:19,445 - INFO: Making seed reads finished.

2020-08-07 10:33:19,445 - INFO: Checking seed reads and parameters ...
2020-08-07 10:33:19,445 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2020-08-07 10:33:19,445 - INFO: If the result graph is not a circular organelle genome,
2020-08-07 10:33:19,445 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2020-08-07 10:33:29,327 - INFO: Pre-assembling mapped reads ...
2020-08-07 10:53:15,412 - WARNING: Pre-assembling failed. The estimations for embplant_mt-hitting base-coverage and word size may be misleading.
2020-08-07 10:53:15,759 - INFO: Estimated embplant_mt-hitting base-coverage = 430.20
2020-08-07 10:53:16,017 - INFO: Reads reduced to = 27204814+27204814
2020-08-07 10:53:16,018 - INFO: Adjusting expected embplant_mt base coverage to 300.00
2020-08-07 10:53:16,018 - INFO: Estimated word size(s): 112
2020-08-07 10:53:16,018 - INFO: Setting '-w 112'
2020-08-07 10:53:16,019 - INFO: Setting '--max-extending-len inf'
2020-08-07 10:53:16,406 - INFO: Checking seed reads and parameters finished.

2020-08-07 10:53:16,406 - INFO: Making read index ...
2020-08-07 10:56:07,212 - INFO: For cszmt/1-CSZ_R1.fq, only top 27204814 reads are used in downstream analysis.
2020-08-07 10:59:04,236 - INFO: For cszmt/2-CSZ_R2.fq, only top 27204814 reads are used in downstream analysis.
2020-08-07 11:00:07,016 - INFO: Mem 18.036 G, 43584031 candidates in all 54409628 reads
2020-08-07 11:00:07,250 - INFO: Pre-grouping reads ...
2020-08-07 11:00:07,250 - INFO: Setting '--pre-w 112'
2020-08-07 11:00:16,205 - INFO: Mem 16.695 G, 6173256/6173256 used/duplicated
2020-08-07 11:27:51,527 - INFO: Mem 119.419 G, 900132 groups made.
2020-08-07 11:30:17,211 - INFO: Making read index finished.

2020-08-07 11:30:17,212 - INFO: Extending ...
2020-08-07 11:30:17,212 - INFO: Adding initial words ...
2020-08-07 11:30:22,253 - INFO: AW 1521062
2020-08-07 11:34:17,675 - INFO: Round 1: 43584031/43584031 AI 1017813 AW 5079820 Mem 88.776
2020-08-07 11:37:46,124 - INFO: Round 2: 43584031/43584031 AI 1074116 AW 5540534 Mem 88.776
2020-08-07 11:41:20,177 - INFO: Round 3: 43584031/43584031 AI 1298972 AW 6829594 Mem 88.776
2020-08-07 11:45:04,361 - INFO: Round 4: 43584031/43584031 AI 2183731 AW 12378778 Mem 89.276
2020-08-07 11:48:44,945 - INFO: Round 5: 43584031/43584031 AI 2579910 AW 15579622 Mem 89.276
2020-08-07 11:52:26,487 - INFO: Round 6: 43584031/43584031 AI 2818105 AW 17476662 Mem 89.276
2020-08-07 11:56:06,324 - INFO: Round 7: 43584031/43584031 AI 2941407 AW 18454056 Mem 89.276
2020-08-07 11:59:45,215 - INFO: Round 8: 43584031/43584031 AI 2998539 AW 18939610 Mem 89.276
2020-08-07 12:07:05,798 - INFO: Hit the round limit 10 and terminated ...
2020-08-07 12:09:18,389 - INFO: Extending finished.

2020-08-07 12:09:21,858 - INFO: Separating filtered fastq file ...
2020-08-07 12:09:53,999 - INFO: Setting '-k 21,55,85,115'
2020-08-07 12:09:53,999 - INFO: Assembling using SPAdes ...
2020-08-07 12:09:55,424 - INFO: spades.py -t 144 -t 144 -m 1800 -1 cszmt/filtered_1_paired.fq -2 cszmt/filtered_2_paired.fq --s1 cszmt/filtered_1_unpaired.fq --s2 cszmt/filtered_2_unpaired.fq -k 21,55,85,115 -o cszmt/filtered_spades
2020-08-07 12:17:18,977 - ERROR: Error in SPAdes:
== Error == system call for: "['/home/lst/miniconda3/share/spades-3.13.0-0/bin/spades-core', '/media/lst/ed8412ea-f84d-40b5-b433-1a157fbfbe7d/chenshuzhangmt/Cleandata/get/cszmt/filtered_spades/K21/configs/config.info']" finished abnormally, err code: -6

2020-08-07 12:17:18,978 - ERROR: Assembling failed.

Total cost 7452.91 s
Thank you!

I installed the GetOrganelle c by conda, the spades.py --test was susscesful.
Please help me to fix this issue.

Too many results due to palindromic repeats

Hi, @Kinggerm,
I am trying to use GetOrganelle to assemble the chloroplast of my plant. In the process，I got 512 results. However,I don’t know how to choose the best one.
Here is the full log:

GetOrganelle v1.6.2

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 2.7.5 (default, Jul 13 2018, 13:06:57) [GCC 4.8.5 20150623 (Red Hat 4.8.5-28)]
Python libs: numpy 1.15.2; sympy 1.4; scipy 1.2.2
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
/tmp/user249/GetOrganelle-master/get_organelle_from_reads.py -1 Nitella-fuiana_FDSW190040255-1a_1.clean.fq.gz -2 Nitella-fuiana_FDSW190040255-1a_2.clean.fq.gz -o plastome_output2 -R 15 -k 21,45,65,85,105 -F embplant_pt

2019-06-27 16:41:58,344 - INFO: Pre-reading fastq ...
2019-06-27 16:41:58,345 - INFO: Estimating reads to use ...
2019-06-27 16:41:59,763 - INFO: Tasting 100000+100000 reads ...
2019-06-27 16:42:14,178 - INFO: Estimating reads to use finished.
2019-06-27 16:42:14,180 - INFO: Unzipping reads file: Nitella-fuiana_FDSW190040255-1a_1.clean.fq.gz (1737988090 bytes)
2019-06-27 16:42:39,201 - INFO: Unzipping reads file: Nitella-fuiana_FDSW190040255-1a_2.clean.fq.gz (1856381193 bytes)
2019-06-27 16:43:04,840 - INFO: Counting read qualities ...
2019-06-27 16:43:05,063 - INFO: Identified quality encoding format = Illumina 1.8+
2019-06-27 16:43:05,067 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2019-06-27 16:43:05,162 - INFO: Mean error rate = 0.0034
2019-06-27 16:43:05,165 - INFO: Counting read lengths ...
2019-06-27 16:43:46,480 - INFO: Mean = 149.0 bp, maximum = 150 bp.
2019-06-27 16:43:46,482 - INFO: Reads used = 9209044+9209044
2019-06-27 16:43:46,482 - INFO: Pre-reading fastq finished.

2019-06-27 16:43:46,483 - INFO: Making seed reads ...
2019-06-27 16:43:46,486 - INFO: Seed bowtie2 index existed!
2019-06-27 16:43:46,486 - INFO: Mapping reads to seed bowtie2 index ...
2019-06-27 16:53:13,473 - INFO: Mapping finished.
2019-06-27 16:53:13,474 - INFO: Seed reads made: plastome_output2/seed/embplant_pt.initial.fq (13948724 bytes)
2019-06-27 16:53:13,475 - INFO: Making seed reads finished.

2019-06-27 16:53:13,476 - INFO: Checking seed reads and parameters ...
2019-06-27 16:53:13,476 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2019-06-27 16:53:13,477 - INFO: If the result graph is not a circular organelle genome,
2019-06-27 16:53:13,477 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2019-06-27 16:53:20,015 - INFO: Pre-assembling mapped reads ...
2019-06-27 16:53:34,726 - INFO: Pre-assembling mapped reads finished.
2019-06-27 16:53:34,727 - INFO: Estimated embplant_pt-hitting base-coverage = 1182.87
2019-06-27 16:53:34,728 - INFO: Reads reduced to = 3892673+3892673
2019-06-27 16:53:34,728 - INFO: Adjusting expected embplant_pt base coverage to 500.00
2019-06-27 16:53:34,729 - INFO: Estimated word size(s): 111
2019-06-27 16:53:34,729 - INFO: Setting '-w 111'
2019-06-27 16:53:34,730 - INFO: Setting '--max-extending-len inf'
2019-06-27 16:53:34,974 - INFO: Checking seed reads and parameters finished.

2019-06-27 16:53:34,976 - INFO: Making read index ...
2019-06-27 16:54:35,825 - INFO: For plastome_output2/1-Nitella-fuiana_FDSW190040255-1a_1.clean.fq.gz.fastq, only top 3892673 reads are used in downstream analysis.
2019-06-27 16:55:36,381 - INFO: For plastome_output2/2-Nitella-fuiana_FDSW190040255-1a_2.clean.fq.gz.fastq, only top 3892673 reads are used in downstream analysis.
2019-06-27 16:55:46,930 - INFO: 6417111 candidates in all 7785346 reads
2019-06-27 16:55:46,956 - INFO: Pre-grouping reads ...
2019-06-27 16:55:46,957 - INFO: Setting '--pre-w 111'
2019-06-27 16:55:49,867 - INFO: 200000/1000496 used/duplicated
2019-06-27 16:56:15,625 - INFO: 1061 groups made.
2019-06-27 16:56:16,949 - INFO: Making read index finished.

2019-06-27 16:56:17,116 - INFO: Extending ...
2019-06-27 16:56:17,120 - INFO: Adding initial words ...
2019-06-27 16:56:18,680 - INFO: AW 256854
2019-06-27 16:57:21,367 - INFO: Round 1: 6417111/6417111 AI 116029 AW 805462
2019-06-27 16:58:25,368 - INFO: Round 2: 6417111/6417111 AI 156185 AW 989754
2019-06-27 16:59:28,833 - INFO: Round 3: 6417111/6417111 AI 170285 AW 1058468
2019-06-27 17:00:32,138 - INFO: Round 4: 6417111/6417111 AI 172792 AW 1070134
2019-06-27 17:01:35,321 - INFO: Round 5: 6417111/6417111 AI 172830 AW 1070508
2019-06-27 17:02:38,258 - INFO: Round 6: 6417111/6417111 AI 172839 AW 1070750
2019-06-27 17:03:41,602 - INFO: Round 7: 6417111/6417111 AI 172846 AW 1070920
2019-06-27 17:04:45,846 - INFO: Round 8: 6417111/6417111 AI 172853 AW 1071032
2019-06-27 17:05:49,208 - INFO: Round 9: 6417111/6417111 AI 172854 AW 1071072
2019-06-27 17:06:54,784 - INFO: Round 10: 6417111/6417111 AI 172854 AW 1071072
2019-06-27 17:06:54,786 - INFO: No more reads found and terminated ...
2019-06-27 17:07:27,185 - INFO: Extending finished.

2019-06-27 17:07:27,187 - INFO: Separating filtered fastq file ...
2019-06-27 17:07:29,817 - INFO: Setting '-k 21,45,65,85,105'
2019-06-27 17:07:29,818 - INFO: Assembling using SPAdes ...
2019-06-27 17:12:24,214 - INFO: Insert size = 370.581, deviation = 74.658, left quantile = 277, right quantile = 465
2019-06-27 17:12:24,215 - INFO: Assembling finished.

2019-06-27 17:12:24,216 - INFO: Slimming assembly graphs ...
2019-06-27 17:12:26,244 - INFO: Slimming plastome_output2/filtered_spades/K105/assembly_graph.fastg finished!
2019-06-27 17:12:28,206 - INFO: Slimming plastome_output2/filtered_spades/K85/assembly_graph.fastg finished!
2019-06-27 17:12:30,174 - INFO: Slimming plastome_output2/filtered_spades/K65/assembly_graph.fastg finished!
2019-06-27 17:12:32,142 - INFO: Slimming plastome_output2/filtered_spades/K45/assembly_graph.fastg finished!
2019-06-27 17:12:32,143 - INFO: Slimming assembly graphs finished

2019-06-27 17:12:32,144 - INFO: Extracting embplant_pt from the assemblies ...
2019-06-27 17:12:32,149 - INFO: Disentangling plastome_output2/filtered_spades/K105/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2019-06-27 17:22:32,150 - INFO: Disentangling timeout. (see '--disentangle-time-limit' for more)
2019-06-27 17:22:32,152 - INFO: Disentangling plastome_output2/filtered_spades/K85/assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg as a circular genome ...
2019-06-27 17:25:18,777 - INFO: Vertex_2654 #copy = 1
2019-06-27 17:25:18,778 - INFO: Vertex_32157 #copy = 1
2019-06-27 17:25:18,779 - INFO: Vertex_32228 #copy = 1
2019-06-27 17:25:18,780 - INFO: Vertex_33112 #copy = 1
2019-06-27 17:25:18,780 - INFO: Vertex_35113 #copy = 1
2019-06-27 17:25:18,781 - INFO: Vertex_35677 #copy = 1
2019-06-27 17:25:18,781 - INFO: Vertex_35783 #copy = 1
2019-06-27 17:25:18,782 - INFO: Vertex_35851 #copy = 1
2019-06-27 17:25:18,783 - INFO: Vertex_35897 #copy = 1
2019-06-27 17:25:18,783 - INFO: Vertex_35903 #copy = 1
2019-06-27 17:25:18,784 - INFO: Vertex_35939 #copy = 1
2019-06-27 17:25:18,785 - INFO: Vertex_35951 #copy = 1
2019-06-27 17:25:18,785 - INFO: Vertex_35957 #copy = 1
2019-06-27 17:25:18,786 - INFO: Vertex_35963 #copy = 2
2019-06-27 17:25:18,787 - INFO: Vertex_35969 #copy = 2
2019-06-27 17:25:18,787 - INFO: Vertex_5158 #copy = 2
2019-06-27 17:25:18,788 - INFO: Vertex_5244 #copy = 1
2019-06-27 17:25:18,788 - INFO: Vertex_5590 #copy = 1
2019-06-27 17:25:18,789 - INFO: Vertex_8058 #copy = 1
2019-06-27 17:25:18,789 - INFO: Average embplant_pt kmer-coverage = 150.721
2019-06-27 17:25:18,789 - INFO: Average embplant_pt base-coverage = 345.499
2019-06-27 17:25:18,790 - INFO: Writing output ...
2019-06-27 17:25:19,493 - WARNING: Multiple circular genome structures produced!
2019-06-27 17:25:19,494 - WARNING: Please check the existence of those isomers by using reads mapping (library information) or longer reads.
2019-06-27 17:25:19,502 - INFO: Writing PATH1 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.1.path_sequence.fasta
2019-06-27 17:25:19,509 - INFO: Writing PATH2 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.2.path_sequence.fasta
2019-06-27 17:25:19,516 - INFO: Writing PATH3 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.3.path_sequence.fasta
2019-06-27 17:25:19,523 - INFO: Writing PATH4 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.4.path_sequence.fasta
2019-06-27 17:25:19,530 - INFO: Writing PATH5 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.5.path_sequence.fasta
2019-06-27 17:25:19,538 - INFO: Writing PATH6 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.6.path_sequence.fasta
2019-06-27 17:25:19,545 - INFO: Writing PATH7 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.7.path_sequence.fasta
2019-06-27 17:25:19,551 - INFO: Writing PATH8 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.8.path_sequence.fasta
2019-06-27 17:25:19,558 - INFO: Writing PATH9 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.9.path_sequence.fasta
2019-06-27 17:25:19,565 - INFO: Writing PATH10 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.10.path_sequence.fasta
2019-06-27 17:25:19,573 - INFO: Writing PATH11 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.11.path_sequence.fasta
2019-06-27 17:25:19,579 - INFO: Writing PATH12 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.12.path_sequence.fasta
2019-06-27 17:25:19,586 - INFO: Writing PATH13 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.13.path_sequence.fasta
2019-06-27 17:25:19,593 - INFO: Writing PATH14 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.14.path_sequence.fasta
2019-06-27 17:25:19,600 - INFO: Writing PATH15 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.15.path_sequence.fasta
2019-06-27 17:25:19,607 - INFO: Writing PATH16 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.16.path_sequence.fasta
2019-06-27 17:25:19,614 - INFO: Writing PATH17 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.17.path_sequence.fasta
2019-06-27 17:25:19,621 - INFO: Writing PATH18 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.18.path_sequence.fasta
2019-06-27 17:25:19,628 - INFO: Writing PATH19 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.19.path_sequence.fasta
2019-06-27 17:25:19,635 - INFO: Writing PATH20 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.20.path_sequence.fasta
2019-06-27 17:25:19,643 - INFO: Writing PATH21 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.21.path_sequence.fasta
2019-06-27 17:25:19,650 - INFO: Writing PATH22 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.22.path_sequence.fasta
2019-06-27 17:25:19,656 - INFO: Writing PATH23 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.23.path_sequence.fasta
2019-06-27 17:25:19,663 - INFO: Writing PATH24 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.24.path_sequence.fasta
2019-06-27 17:25:19,670 - INFO: Writing PATH25 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.25.path_sequence.fasta
2019-06-27 17:25:19,677 - INFO: Writing PATH26 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.26.path_sequence.fasta
2019-06-27 17:25:19,684 - INFO: Writing PATH27 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.27.path_sequence.fasta
2019-06-27 17:25:19,691 - INFO: Writing PATH28 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.28.path_sequence.fasta
2019-06-27 17:25:19,698 - INFO: Writing PATH29 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.29.path_sequence.fasta
2019-06-27 17:25:19,705 - INFO: Writing PATH30 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.30.path_sequence.fasta
2019-06-27 17:25:19,712 - INFO: Writing PATH31 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.31.path_sequence.fasta
2019-06-27 17:25:19,719 - INFO: Writing PATH32 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.32.path_sequence.fasta
2019-06-27 17:25:19,726 - INFO: Writing PATH33 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.33.path_sequence.fasta
2019-06-27 17:25:19,733 - INFO: Writing PATH34 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.34.path_sequence.fasta
2019-06-27 17:25:19,740 - INFO: Writing PATH35 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.35.path_sequence.fasta
2019-06-27 17:25:19,747 - INFO: Writing PATH36 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.36.path_sequence.fasta
2019-06-27 17:25:19,753 - INFO: Writing PATH37 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.37.path_sequence.fasta
2019-06-27 17:25:19,760 - INFO: Writing PATH38 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.38.path_sequence.fasta
2019-06-27 17:25:19,767 - INFO: Writing PATH39 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.39.path_sequence.fasta
2019-06-27 17:25:19,774 - INFO: Writing PATH40 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.40.path_sequence.fasta
2019-06-27 17:25:19,781 - INFO: Writing PATH41 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.41.path_sequence.fasta
2019-06-27 17:25:19,788 - INFO: Writing PATH42 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.42.path_sequence.fasta
2019-06-27 17:25:19,795 - INFO: Writing PATH43 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.43.path_sequence.fasta
2019-06-27 17:25:19,802 - INFO: Writing PATH44 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.44.path_sequence.fasta
2019-06-27 17:25:19,809 - INFO: Writing PATH45 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.45.path_sequence.fasta
2019-06-27 17:25:19,816 - INFO: Writing PATH46 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.46.path_sequence.fasta
2019-06-27 17:25:19,823 - INFO: Writing PATH47 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.47.path_sequence.fasta
2019-06-27 17:25:19,830 - INFO: Writing PATH48 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.48.path_sequence.fasta
2019-06-27 17:25:19,837 - INFO: Writing PATH49 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.49.path_sequence.fasta
2019-06-27 17:25:19,844 - INFO: Writing PATH50 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.50.path_sequence.fasta
2019-06-27 17:25:19,850 - INFO: Writing PATH51 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.51.path_sequence.fasta
2019-06-27 17:25:19,858 - INFO: Writing PATH52 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.52.path_sequence.fasta
2019-06-27 17:25:19,864 - INFO: Writing PATH53 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.53.path_sequence.fasta
2019-06-27 17:25:19,871 - INFO: Writing PATH54 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.54.path_sequence.fasta
2019-06-27 17:25:19,878 - INFO: Writing PATH55 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.55.path_sequence.fasta
2019-06-27 17:25:19,885 - INFO: Writing PATH56 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.56.path_sequence.fasta
2019-06-27 17:25:19,892 - INFO: Writing PATH57 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.57.path_sequence.fasta
2019-06-27 17:25:19,899 - INFO: Writing PATH58 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.58.path_sequence.fasta
2019-06-27 17:25:19,907 - INFO: Writing PATH59 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.59.path_sequence.fasta
2019-06-27 17:25:19,914 - INFO: Writing PATH60 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.60.path_sequence.fasta
2019-06-27 17:25:19,921 - INFO: Writing PATH61 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.61.path_sequence.fasta
2019-06-27 17:25:19,928 - INFO: Writing PATH62 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.62.path_sequence.fasta
2019-06-27 17:25:19,935 - INFO: Writing PATH63 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.63.path_sequence.fasta
2019-06-27 17:25:19,943 - INFO: Writing PATH64 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.64.path_sequence.fasta
2019-06-27 17:25:19,950 - INFO: Writing PATH65 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.65.path_sequence.fasta
2019-06-27 17:25:19,957 - INFO: Writing PATH66 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.66.path_sequence.fasta
2019-06-27 17:25:19,964 - INFO: Writing PATH67 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.67.path_sequence.fasta
2019-06-27 17:25:19,970 - INFO: Writing PATH68 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.68.path_sequence.fasta
2019-06-27 17:25:19,977 - INFO: Writing PATH69 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.69.path_sequence.fasta
2019-06-27 17:25:19,984 - INFO: Writing PATH70 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.70.path_sequence.fasta
2019-06-27 17:25:19,990 - INFO: Writing PATH71 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.71.path_sequence.fasta
2019-06-27 17:25:19,997 - INFO: Writing PATH72 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.72.path_sequence.fasta
2019-06-27 17:25:20,004 - INFO: Writing PATH73 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.73.path_sequence.fasta
2019-06-27 17:25:20,010 - INFO: Writing PATH74 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.74.path_sequence.fasta
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2019-06-27 17:25:23,013 - INFO: Writing PATH511 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.511.path_sequence.fasta
2019-06-27 17:25:23,019 - INFO: Writing PATH512 of complete embplant_pt to plastome_output2/embplant_pt.K85.complete.graph1.512.path_sequence.fasta
2019-06-27 17:25:23,020 - INFO: Writing GRAPH to plastome_output2/embplant_pt.K85.complete.graph1.selected_graph.gfa
2019-06-27 17:25:23,066 - INFO: Result status of embplant_pt: circular genome
2019-06-27 17:25:23,226 - INFO: Please visualize plastome_output2/filtered_K85.assembly_graph.fastg.extend-embplant_pt-embplant_mt.fastg using Bandage to confirm the final result.
2019-06-27 17:25:23,227 - INFO: Writing output finished.
2019-06-27 17:25:23,229 - INFO: Extracting embplant_pt from the assemblies finished.

Total cost 2605.14 s
Thank you!

And the resulting assembly in Bandage was as follows:

Crashes while running GetOrganelle

Hi,
I would like to extract plant mt genome from the whole raw data sequence. When I use Illumina pair-end reads (9 GB each), it stops suddenly. I tried several times. But the same issues. My server is having 188 GB RAM only. Is it possible to use the subsampling of Illumina RAW reads?

Also, I am having an ONT Nanopore raw data sequence (9 GB). Can I use together here to extract plant mt reads for the assembly using SPAdes?
Please suggest to me.
Thank you.

--genes argument for animal/fungal mitochondrial assembly?

Hi,

Thanks for the great tool. I'm currently trying to assemble animal mitochondria. In the recipes section, the animal and fungal recipes contain "--genes animal_mt_genes.fasta". However, this "--genes" flag is missing from all other recipes.

What exactly is the "--genes" flag doing differently to the "-s" seed flag? Is it necessary? If so, what is meant to be within the "animal_mt_genes.fasta" file? I note that no files in GetOrganelleLib correspond to "animal_mt_genes.fasta", and that I previously assembled an animal mitochondrial genome without including the "--genes" flag.

Thanks,
Charles

AttributeError: 'Process' object has no attribute 'memory_info'

Hi @Kinggerm,

I installed GetOgranelle with these settings on a new cluster that I am using:

GetOrganelle v1.6.2e

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 2.7.5 (default, Nov 20 2015, 02:00:19)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Python libs: numpy 1.7.1; sympy 1.4; scipy 0.12.1; psutil 1.2.1
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
/home/s/simon-hellemans/.local/bin/get_organelle_from_reads.py -1 12740_R1.fastq.gz -2 12740_R2.fastq.gz -s Termes_genome_sequence.fasta.txt --genes Termes_gene_features_sequence.txt -o Cavi_GetOrg -R 3 -k 21,45,65,85,105 -F animal_mt

I launched a first job but there was an issue during the Making read index step:

2019-11-16 11:28:17,483 - INFO: Making read index ...
2019-11-16 11:28:17,486 - INFO: 1 reads���������������������������������������2019-11-16 11:28:18,013 - INFO: 54322 reads�������������������������������������������2019-11-16 11:28:18,541 - INFO: 108643 reads��������������������������������������������2019-11-16 11:28:19,107 - INFO: 162964 reads��������������������������������������������2019-11-16 11:28:19,684 - INFO: 217285 reads��������������������������������������������2019-11-16 11:28:20,311 - INFO: 271606 reads��������������������������������������������2019-11-16 11:28:20,969 - INFO: 325927 reads��������������������������������������������2019-11-16 11:28:21,470 - INFO: 380248 reads��������������������������������������������2019-11-16 11:28:22,188 - INFO: 434569 reads��������������������������������������������2019-11-16 11:28:22,684 - INFO: 488890 reads��������������������������������������������2019-11-16 11:28:23,430 - INFO: 543211 reads��������������������������������������������2019-11-16 11:28:23,917 - INFO: 597532 reads��������������������������������������������2019-11-16 11:28:24,732 - 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INFO: 7822225 reads���������������������������������������������2019-11-16 11:29:45,804 - INFO: 7876546 reads���������������������������������������������2019-11-16 11:29:46,291 - INFO: 7930867 reads���������������������������������������������2019-11-16 11:29:46,773 - INFO: 7985188 reads���������������������������������������������2019-11-16 11:29:47,257 - INFO: 8039509 reads���������������������������������������������2019-11-16 11:29:47,741 - INFO: 8093830 reads���������������������������������������������2019-11-16 11:29:53,255 - INFO: 8148151 reads���������������������������������������������2019-11-16 11:29:53,739 - INFO: 8202472 reads���������������������������������������������2019-11-16 11:29:54,223 - INFO: 8256793 reads���������������������������������������������2019-11-16 11:29:54,708 - INFO: 8311114 reads���������������������������������������������2019-11-16 11:29:55,190 - INFO: 8365435 reads���������������������������������������������2019-11-16 11:29:55,682 - INFO: 8419756 reads���������������������������������������������2019-11-16 11:29:56,166 - INFO: 8474077 reads���������������������������������������������2019-11-16 11:29:56,651 - INFO: 8528398 reads���������������������������������������������2019-11-16 11:29:57,140 - INFO: 8582719 reads���������������������������������������������2019-11-16 11:29:57,627 - INFO: 8637040 reads���������������������������������������������2019-11-16 11:29:58,118 - INFO: 8691361 reads���������������������������������������������2019-11-16 11:29:58,603 - INFO: 8745682 reads���������������������������������������������2019-11-16 11:29:59,090 - INFO: 8800003 reads���������������������������������������������2019-11-16 11:29:59,571 - INFO: 8854324 reads���������������������������������������������2019-11-16 11:30:00,051 - INFO: 8908645 reads���������������������������������������������2019-11-16 11:30:00,539 - INFO: 8962966 reads���������������������������������������������2019-11-16 11:30:01,022 - INFO: 9017287 reads���������������������������������������������2019-11-16 11:30:01,509 - INFO: 9071608 reads���������������������������������������������2019-11-16 11:30:01,996 - INFO: 9125929 reads���������������������������������������������2019-11-16 11:30:02,479 - INFO: 9180250 reads���������������������������������������������2019-11-16 11:30:02,966 - INFO: 9234571 reads���������������������������������������������2019-11-16 11:30:03,449 - INFO: 9288892 reads���������������������������������������������2019-11-16 11:30:03,936 - INFO: 9343213 reads���������������������������������������������2019-11-16 11:30:04,416 - INFO: 9397534 reads���������������������������������������������2019-11-16 11:30:04,899 - INFO: 9451855 reads���������������������������������������������2019-11-16 11:30:05,386 - INFO: 9506176 reads���������������������������������������������2019-11-16 11:30:05,867 - INFO: 9560497 reads���������������������������������������������2019-11-16 11:30:06,352 - INFO: 9614818 reads���������������������������������������������2019-11-16 11:30:06,838 - INFO: 9669139 reads���������������������������������������������2019-11-16 11:30:07,322 - INFO: 9723460 reads���������������������������������������������2019-11-16 11:30:07,811 - INFO: 9777781 reads���������������������������������������������2019-11-16 11:30:08,306 - INFO: 9832102 reads���������������������������������������������2019-11-16 11:30:08,812 - INFO: 9886423 reads���������������������������������������������2019-11-16 11:30:09,313 - INFO: 9940744 reads���������������������������������������������2019-11-16 11:30:09,810 - INFO: 9995065 reads���������������������������������������������2019-11-16 11:30:10,298 - INFO: 10049386 reads����������������������������������������������2019-11-16 11:30:10,781 - INFO: 10103707 reads����������������������������������������������2019-11-16 11:30:17,407 - INFO: 10158028 reads����������������������������������������������2019-11-16 11:30:26,687 - INFO: 10212349 reads����������������������������������������������2019-11-16 11:30:27,180 - INFO: 10266670 reads����������������������������������������������2019-11-16 11:30:27,680 - INFO: 10320991 reads����������������������������������������������2019-11-16 11:30:28,201 - INFO: 10375312 reads����������������������������������������������2019-11-16 11:30:28,703 - INFO: 10429633 reads����������������������������������������������2019-11-16 11:30:29,206 - INFO: 10483954 reads����������������������������������������������2019-11-16 11:30:29,715 - INFO: 10538275 reads����������������������������������������������2019-11-16 11:30:30,248 - INFO: 10592596 reads����������������������������������������������2019-11-16 11:30:30,751 - INFO: 10646917 reads����������������������������������������������2019-11-16 11:30:31,256 - INFO: 10701238 reads����������������������������������������������2019-11-16 11:30:31,770 - INFO: 10755559 reads����������������������������������������������2019-11-16 11:30:32,276 - INFO: 10809880 reads����������������������������������������������2019-11-16 11:30:32,791 - INFO: 10864201 reads����������������������������������������������2019-11-16 11:30:33,338 - INFO: 10918522 reads����������������������������������������������2019-11-16 11:30:33,851 - INFO: 10972843 reads����������������������������������������������2019-11-16 11:30:34,349 - INFO: 11027164 reads����������������������������������������������2019-11-16 11:30:34,563 - ERROR: 
Traceback (most recent call last):
  File "/home/s/simon-hellemans/.local/lib/python2.7/site-packages/GetOrganelle-1.6.2e-py2.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3673, in main
    resume=resume, echo_step=echo_step, log_handler=log_handler)
  File "/home/s/simon-hellemans/.local/lib/python2.7/site-packages/GetOrganelle-1.6.2e-py2.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 1875, in make_read_index
    memory_usage = "Mem " + str(round(this_process.memory_info().rss / 1024.0 / 1024 / 1024, 3)) + " G, "
AttributeError: 'Process' object has no attribute 'memory_info'

Do you know how to solve this?

Thank you in advance for your reply,
Best,
Simon

Issue -F anonym

Hi @Kinggerm,

I wanted to try to assemble the bacterium Wolbachia from paired Illumina reads. So I used the option -F anonym (even though I don't know if it would work considering the size of expected genome; 1Mb); and I get the following error:

GetOrganelle v1.6.2

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0]
Python libs: numpy 1.17.0; sympy 1.4; scipy 1.3.0
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
/home/ulb/ebe/dfournie/miniconda3/bin/get_organelle_from_reads.py -1 213-Cavi-1_S1_R1_paired.fastq -2 213-Cavi-1_S1_R2_paired.fastq -o Wolbachia_S1_output -s wCle_genome.fasta --genes wCle_features.fasta -R 3 -k 21,45,65,85,105 -F anonym

2019-07-31 20:25:08,651 - INFO: Setting '--target-genome-size [3983366]' for estimating the word size value for anonym type.
2019-07-31 20:25:08,694 - INFO: Setting '--expected-max-size [19916830]' for estimating the word size value for anonym type.
2019-07-31 20:25:08,955 - INFO: Pre-reading fastq ...
2019-07-31 20:25:08,955 - INFO: Estimating reads to use ...
2019-07-31 20:25:10,930 - ERROR:
Traceback (most recent call last):
File "/home/users/d/f/dfournie/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3541, in main
random_seed=options.random_seed, verbose_log=options.verbose_log, log_handler=log_handler)
File "/home/users/d/f/dfournie/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 915, in estimate_maximum_n_reads_using_mapping
/ max_organelle_base_percent * GUESSING_FQ_SEQ_INFLATE_TO_FILE
KeyError: 'anonym'

Is it something to be done here?

Thanks in advance,
Simon

more than one final fasta file

Hi:
I successfully assembled the plastid genome using GetOrganelle, however the output contains four fasta files, 1.1fasta, 1.2fasta, 1.3fasta and 1.4fasta. I checked the gfa file and it looks like this:

it contains 3 single copy regions and 3 repeat regions. Judging by the depth, one repeat region (the smallest one) appear three times and the other two appear two times. Since this plastid genome is different from the quadripartite structure, could this caused by assemble errors?

Many thanks!

INFO: Hit the round limit 50 and terminated

Hi Jianjun,

I tried the GetOrganelle to assemble the mt and cp genomes. I have 12 Gb of paired-end reads. The software succussed to assemble the cp genome. However, I got errors when I assemble the mt genome.
2020-09-17 08:13:45,180 - INFO: Round 42: 60159839/60159839 AI 20384110 AW 625364994 Mem 105.462
2020-09-17 08:25:13,259 - INFO: Round 43: 60159839/60159839 AI 20384880 AW 625393244 Mem 105.465
2020-09-17 08:36:41,316 - INFO: Round 44: 60159839/60159839 AI 20385783 AW 625425476 Mem 105.469
2020-09-17 08:48:11,075 - INFO: Round 45: 60159839/60159839 AI 20386654 AW 625453826 Mem 105.472
2020-09-17 09:00:12,338 - INFO: Round 46: 60159839/60159839 AI 20387288 AW 625475148 Mem 105.475
2020-09-17 09:13:21,565 - INFO: Round 47: 60159839/60159839 AI 20387718 AW 625491504 Mem 105.477
2020-09-17 09:25:39,332 - INFO: Round 48: 60159839/60159839 AI 20388336 AW 625513576 Mem 105.48
2020-09-17 09:37:55,564 - INFO: Round 49: 60159839/60159839 AI 20388904 AW 625535742 Mem 105.483
2020-09-17 09:50:17,657 - INFO: Round 50: 60159839/60159839 AI 20389564 AW 625558416 Mem 105.485
2020-09-17 09:50:17,657 - INFO: Hit the round limit 50 and terminated ...

Could you kindly help me with this error?

Thanks a lot.

Best,

Lingyun

Crashed with SPAdes error

Output:

2020-11-19 15:52:37,727 - INFO: Extending ...
2020-11-19 15:52:37,727 - INFO: Adding initial words ...
2020-11-19 15:52:41,010 - INFO: AW 1157586
2020-11-19 15:52:42,466 - INFO: Round 1: 240758/240758 AI 48459 AW 1194647
2020-11-19 15:52:43,200 - INFO: Round 2: 240758/240758 AI 50521 AW 1210915
2020-11-19 15:52:43,883 - INFO: Round 3: 240758/240758 AI 51479 AW 1220253
2020-11-19 15:52:44,612 - INFO: Round 4: 240758/240758 AI 52154 AW 1226555
2020-11-19 15:52:45,304 - INFO: Round 5: 240758/240758 AI 52492 AW 1230191
2020-11-19 15:52:45,988 - INFO: Round 6: 240758/240758 AI 52700 AW 1232685
2020-11-19 15:52:46,639 - INFO: Round 7: 240758/240758 AI 52856 AW 1234869
2020-11-19 15:52:47,376 - INFO: Round 8: 240758/240758 AI 52972 AW 1236239
2020-11-19 15:52:48,066 - INFO: Round 9: 240758/240758 AI 53023 AW 1236643
2020-11-19 15:52:48,771 - INFO: Round 10: 240758/240758 AI 53034 AW 1236685
2020-11-19 15:52:49,454 - INFO: Round 11: 240758/240758 AI 53039 AW 1236753
2020-11-19 15:52:50,123 - INFO: Round 12: 240758/240758 AI 53042 AW 1236821
2020-11-19 15:52:50,788 - INFO: Round 13: 240758/240758 AI 53042 AW 1236821
2020-11-19 15:52:50,788 - INFO: No more reads found and terminated ...
2020-11-19 15:52:51,528 - INFO: Extending finished.

2020-11-19 15:52:51,555 - INFO: Separating filtered fastq file ... 
2020-11-19 15:52:51,889 - INFO: Setting '-k 21,55,85'
2020-11-19 15:52:51,890 - INFO: Assembling using SPAdes ...
2020-11-19 15:52:51,924 - INFO: spades.py -t 100  -1 duni_sample_15_76_ref_lacertida_mtDNA/filtered_1_paired.fq -2 duni_sample_15_76_ref_lacertida_mtDNA/filtered_2_paired.fq --s1 duni_sample_15_76_ref_lacertida_mtDNA/filtered_1_unpaired.fq --s2 duni_sample_15_76_ref_lacertida_mtDNA/filtered_2_unpaired.fq -k 21,55,85 -o duni_sample_15_76_ref_lacertida_mtDNA/filtered_spades
2020-11-19 15:53:12,323 - ERROR: Error in SPAdes: 
== Error ==  system call for: "['/home/akomissarov/libs/anaconda2/bin/spades-core', '/media/eternus1/data/lizards/forNCBI/mtDNA/duni_sample_15_76_ref_lacertida_mtDNA/filtered_spades/K55/configs/config.info']" finished abnormally, OS return value: -6


2020-11-19 15:53:12,323 - ERROR: Assembling failed.

Total cost 154.74 s

get_organelle_from_assembly.py: no slimmed_assembly_graph found

hi everyone, i'm trying to evaluate the mithocondrial DNA of my sample (fusarium sp.);
i performed the assembly with flye tool on galaxy.eu and use the fastg file produced by the tool.
i always get this error and i can't go on, can you help me? what i'm doing wrong?

HERE THE LOG.TXT FILE:
GetOrganelle v1.7.1a

get_organelle_from_assembly.py isolates organelle genomes from assembly graph.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.8.2 (default, Mar 13 2020, 10:14:16) [GCC 9.3.0]
PYTHON LIBS: GetOrganelleLib 1.7.1a; numpy 1.17.4; sympy 1.5.1; scipy 1.3.3
DEPENDENCIES: Blast 2.9.0
LABEL DB: fungus_mt 0.0.0
WORKING DIR: /home/luca/GetOrganelle
get_organelle_from_assembly.py -F fungus_mt -g seitu.fastg -o risultati/mitoF31

2020-08-07 09:00:50,485 - INFO: Processing assembly graph ...
2020-08-07 09:00:51,011 - INFO: Processing assembly graph finished.

2020-08-07 09:00:51,011 - INFO: Slimming assembly graph ...
2020-08-07 09:00:51,053 - INFO: Slimming risultati/mitoF31/initial_assembly_graph.fastg finished!
2020-08-07 09:00:51,053 - ERROR:
Traceback (most recent call last):
File "get_organelle_from_assembly.py", line 988, in main
if os.path.getsize(slimmed_graph_file) == 0:
File "/usr/lib/python3.8/genericpath.py", line 50, in getsize
return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: 'risultati/mitoF31/slimmed_assembly_graph.fastg'

Total cost 3.71 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

THANK'S EVERYONE

IndexError: list out of range

Hello,

I just tried your tool, which looks quite useful, and everything runned fine until I got the following error:
File "/home/katerina87/miniconda3/bin/get_organelle_from_reads.py", line 3482, in main
expected_maximum_size=options.expected_max_size[go_t],
IndexError: list index out of range

The command I run was

get_organelle_from_reads.py -1 VM3-16_S1_R1.pick.fastq -2 VM3-16_S1_R2.pick.fastq -s Chloroplast.pick.fasta -o GetO_S1_assembly -F other_pt

The reference fasta I am using is from the same species.

Any help or hint on the error would be very helpful.
Thank you!

Failure in slimming fastg

Operating System: macOS Catalina V10.15.6
Codes:

get_organelle_from_reads.py -1 W2M.2_R1_trimmed.fastq.gz -2 W2M.2_R2_trimmed.fastq.gz -F animal_mt -o raw_mtgenome -t 4 -s ../F1_mt_sequences.fasta

Here is the get_org.log.txt

GetOrganelle v1.7.0

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.7 (default, May 6 2020, 04:59:01) [Clang 4.0.1 (tags/RELEASE_401/final)]
PYTHON LIBS: GetOrganelleLib 1.7.0; numpy 1.18.5; sympy 1.6.1; scipy 1.5.0
DEPENDENCIES: Bowtie2 2.3.5.1; SPAdes 3.12.0; Blast 2.6.0
LABEL DB: animal_mt 0.0.0
WORKING DIR: /Users/zzx/Documents/wasps/F1(F.obtusifolia,W2M.2)
/Users/zzx/anaconda3/envs/bioconda/bin/get_organelle_from_reads.py -1 W2M.2_R1_trimmed.fastq.gz -2 W2M.2_R2_trimmed.fastq.gz -F animal_mt -o raw_mtgenome -t 4 -s ../F1_mt_sequences.fasta

2020-07-21 17:00:47,161 - INFO: Pre-reading fastq ...
2020-07-21 17:00:47,161 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-07-21 17:00:47,277 - INFO: Tasting 100000+100000 reads ...
2020-07-21 17:00:53,140 - INFO: Estimating reads to use finished.
2020-07-21 17:00:53,140 - INFO: Unzipping reads file: W2M.2_R1_trimmed.fastq.gz (3801285450 bytes)
2020-07-21 17:01:15,974 - INFO: Unzipping reads file: W2M.2_R2_trimmed.fastq.gz (4141147876 bytes)
2020-07-21 17:01:39,293 - INFO: Counting read qualities ...
2020-07-21 17:01:39,428 - INFO: Identified quality encoding format = Illumina 1.8+
2020-07-21 17:01:39,429 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2020-07-21 17:01:39,488 - INFO: Mean error rate = 0.0043
2020-07-21 17:01:39,489 - INFO: Counting read lengths ...
2020-07-21 17:02:27,611 - INFO: Mean = 145.7 bp, maximum = 151 bp.
2020-07-21 17:02:27,612 - INFO: Reads used = 19983821+20016206
2020-07-21 17:02:27,612 - INFO: Pre-reading fastq finished.

2020-07-21 17:02:27,612 - INFO: Making seed reads ...
2020-07-21 17:02:27,617 - INFO: Making seed - bowtie2 index ...
2020-07-21 17:02:27,757 - INFO: Making seed - bowtie2 index finished.
2020-07-21 17:02:27,757 - INFO: Mapping reads to seed bowtie2 index ...
2020-07-21 17:05:55,457 - INFO: Mapping finished.
2020-07-21 17:05:55,458 - INFO: Seed reads made: raw_mtgenome/seed/animal_mt.initial.fq (1024219 bytes)
2020-07-21 17:05:55,458 - INFO: Making seed reads finished.

2020-07-21 17:05:55,458 - INFO: Checking seed reads and parameters ...
2020-07-21 17:05:55,458 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2020-07-21 17:05:55,458 - INFO: If the result graph is not a circular organelle genome,
2020-07-21 17:05:55,458 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2020-07-21 17:05:55,795 - INFO: Pre-assembling mapped reads ...
2020-07-21 17:11:58,405 - WARNING: Pre-assembling failed. The estimations for animal_mt-hitting base-coverage and word size may be misleading.
2020-07-21 17:11:58,408 - INFO: Estimated animal_mt-hitting base-coverage = 585.01
2020-07-21 17:11:58,548 - INFO: Reads reduced to = 17079896+17107575
2020-07-21 17:11:58,548 - INFO: Adjusting expected animal_mt base coverage to 500.00
2020-07-21 17:11:58,549 - INFO: Estimated word size(s): 116
2020-07-21 17:11:58,549 - INFO: Setting '-w 116'
2020-07-21 17:11:58,549 - INFO: Setting '--max-extending-len inf'
2020-07-21 17:11:58,552 - INFO: Checking seed reads and parameters finished.

2020-07-21 17:11:58,552 - INFO: Making read index ...
2020-07-21 17:13:39,355 - INFO: For raw_mtgenome/1-W2M.2_R1_trimmed.fastq.gz.fastq, only top 17079896 reads are used in downstream analysis.
2020-07-21 17:15:27,384 - INFO: For raw_mtgenome/2-W2M.2_R2_trimmed.fastq.gz.fastq, only top 17107575 reads are used in downstream analysis.
2020-07-21 17:15:50,125 - INFO: 30960099 candidates in all 34187471 reads
2020-07-21 17:15:50,209 - INFO: Pre-grouping reads ...
2020-07-21 17:15:50,209 - INFO: Setting '--pre-w 116'
2020-07-21 17:15:52,872 - INFO: 200000/1003974 used/duplicated
2020-07-21 17:16:12,156 - INFO: 4136 groups made.
2020-07-21 17:16:17,132 - INFO: Making read index finished.

2020-07-21 17:16:17,133 - INFO: Extending ...
2020-07-21 17:16:17,133 - INFO: Adding initial words ...
2020-07-21 17:16:17,195 - INFO: AW 49052
2020-07-21 17:18:27,702 - INFO: Round 1: 30960099/30960099 AI 9911 AW 100560
2020-07-21 17:20:41,988 - INFO: Round 2: 30960099/30960099 AI 14248 AW 138194
2020-07-21 17:22:50,081 - INFO: Round 3: 30960099/30960099 AI 15433 AW 156064
2020-07-21 17:25:10,545 - INFO: Round 4: 30960099/30960099 AI 16081 AW 167542
2020-07-21 17:27:31,953 - INFO: Round 5: 30960099/30960099 AI 17687 AW 184372
2020-07-21 17:29:48,009 - INFO: Round 6: 30960099/30960099 AI 19228 AW 200436
2020-07-21 17:32:04,359 - INFO: Round 7: 30960099/30960099 AI 20364 AW 216006
2020-07-21 17:34:23,215 - INFO: Round 8: 30960099/30960099 AI 21622 AW 232268
2020-07-21 17:36:48,199 - INFO: Round 9: 30960099/30960099 AI 23430 AW 256698
2020-07-21 17:39:09,800 - INFO: Round 10: 30960099/30960099 AI 25249 AW 284960
2020-07-21 17:41:31,142 - INFO: Round 11: 30960099/30960099 AI 27303 AW 314488
2020-07-21 17:43:51,945 - INFO: Round 12: 30960099/30960099 AI 28837 AW 337984
2020-07-21 17:46:16,005 - INFO: Round 13: 30960099/30960099 AI 29801 AW 354218
2020-07-21 17:48:35,112 - INFO: Round 14: 30960099/30960099 AI 30560 AW 366176
2020-07-21 17:50:49,023 - INFO: Round 15: 30960099/30960099 AI 31155 AW 375604
2020-07-21 17:53:05,157 - INFO: Round 16: 30960099/30960099 AI 31585 AW 382226
2020-07-21 17:55:21,726 - INFO: Round 17: 30960099/30960099 AI 31774 AW 385998
2020-07-21 17:57:42,935 - INFO: Round 18: 30960099/30960099 AI 32054 AW 390454
2020-07-21 18:00:09,451 - INFO: Round 19: 30960099/30960099 AI 32307 AW 394340
2020-07-21 18:02:35,411 - INFO: Round 20: 30960099/30960099 AI 32730 AW 400198
2020-07-21 18:04:56,767 - INFO: Round 21: 30960099/30960099 AI 33106 AW 405490
2020-07-21 18:07:16,234 - INFO: Round 22: 30960099/30960099 AI 33331 AW 409536
2020-07-21 18:09:36,640 - INFO: Round 23: 30960099/30960099 AI 33592 AW 413208
2020-07-21 18:11:53,406 - INFO: Round 24: 30960099/30960099 AI 33837 AW 416380
2020-07-21 18:14:05,717 - INFO: Round 25: 30960099/30960099 AI 34055 AW 419710
2020-07-21 18:16:18,959 - INFO: Round 26: 30960099/30960099 AI 34396 AW 424514
2020-07-21 18:18:31,378 - INFO: Round 27: 30960099/30960099 AI 34659 AW 428078
2020-07-21 18:20:44,498 - INFO: Round 28: 30960099/30960099 AI 34929 AW 432170
2020-07-21 18:22:57,282 - INFO: Round 29: 30960099/30960099 AI 35128 AW 435348
2020-07-21 18:25:10,398 - INFO: Round 30: 30960099/30960099 AI 35578 AW 441468
2020-07-21 18:27:22,285 - INFO: Round 31: 30960099/30960099 AI 36045 AW 447784
2020-07-21 18:29:37,794 - INFO: Round 32: 30960099/30960099 AI 36288 AW 451720
2020-07-21 18:32:04,931 - INFO: Round 33: 30960099/30960099 AI 36438 AW 454300
2020-07-21 18:34:28,167 - INFO: Round 34: 30960099/30960099 AI 36605 AW 456692
2020-07-21 18:36:42,344 - INFO: Round 35: 30960099/30960099 AI 36850 AW 460434
2020-07-21 18:38:56,157 - INFO: Round 36: 30960099/30960099 AI 37122 AW 464976
2020-07-21 18:41:14,619 - INFO: Round 37: 30960099/30960099 AI 37298 AW 467784
2020-07-21 18:43:41,084 - INFO: Round 38: 30960099/30960099 AI 37404 AW 469582
2020-07-21 18:46:07,423 - INFO: Round 39: 30960099/30960099 AI 37543 AW 471286
2020-07-21 18:48:30,053 - INFO: Round 40: 30960099/30960099 AI 37798 AW 474110
2020-07-21 18:50:50,503 - INFO: Round 41: 30960099/30960099 AI 38030 AW 476488
2020-07-21 18:53:13,492 - INFO: Round 42: 30960099/30960099 AI 38070 AW 477100
2020-07-21 18:55:36,365 - INFO: Round 43: 30960099/30960099 AI 38127 AW 478000
2020-07-21 18:57:56,929 - INFO: Round 44: 30960099/30960099 AI 38330 AW 480744
2020-07-21 19:00:20,450 - INFO: Round 45: 30960099/30960099 AI 38607 AW 484336
2020-07-21 19:02:47,600 - INFO: Round 46: 30960099/30960099 AI 38984 AW 489700
2020-07-21 19:05:11,826 - INFO: Round 47: 30960099/30960099 AI 39379 AW 495220
2020-07-21 19:07:35,999 - INFO: Round 48: 30960099/30960099 AI 39718 AW 499892
2020-07-21 19:09:57,396 - INFO: Round 49: 30960099/30960099 AI 39975 AW 503412
2020-07-21 19:12:12,979 - INFO: Round 50: 30960099/30960099 AI 40273 AW 507324
2020-07-21 19:14:34,750 - INFO: Round 51: 30960099/30960099 AI 40420 AW 509332
2020-07-21 19:16:55,997 - INFO: Round 52: 30960099/30960099 AI 40559 AW 511434
2020-07-21 19:19:22,955 - INFO: Round 53: 30960099/30960099 AI 40676 AW 513330
2020-07-21 19:21:47,038 - INFO: Round 54: 30960099/30960099 AI 40723 AW 514038
2020-07-21 19:24:13,280 - INFO: Round 55: 30960099/30960099 AI 40738 AW 514328
2020-07-21 19:26:41,299 - INFO: Round 56: 30960099/30960099 AI 40740 AW 514336
2020-07-21 19:29:07,592 - INFO: Round 57: 30960099/30960099 AI 40801 AW 515170
2020-07-21 19:31:31,771 - INFO: Round 58: 30960099/30960099 AI 40859 AW 515992
2020-07-21 19:33:50,559 - INFO: Round 59: 30960099/30960099 AI 41042 AW 518264
2020-07-21 19:36:09,275 - INFO: Round 60: 30960099/30960099 AI 41242 AW 521350
2020-07-21 19:38:27,989 - INFO: Round 61: 30960099/30960099 AI 41436 AW 523988
2020-07-21 19:40:46,108 - INFO: Round 62: 30960099/30960099 AI 41529 AW 525788
2020-07-21 19:43:05,304 - INFO: Round 63: 30960099/30960099 AI 41621 AW 527462
2020-07-21 19:45:24,022 - INFO: Round 64: 30960099/30960099 AI 41684 AW 528500
2020-07-21 19:47:43,031 - INFO: Round 65: 30960099/30960099 AI 41722 AW 529068
2020-07-21 19:50:02,303 - INFO: Round 66: 30960099/30960099 AI 41752 AW 529626
2020-07-21 19:52:20,581 - INFO: Round 67: 30960099/30960099 AI 41785 AW 530088
2020-07-21 19:54:39,303 - INFO: Round 68: 30960099/30960099 AI 41815 AW 530706
2020-07-21 19:56:57,682 - INFO: Round 69: 30960099/30960099 AI 41842 AW 531130
2020-07-21 19:59:16,667 - INFO: Round 70: 30960099/30960099 AI 41920 AW 531934
2020-07-21 20:01:35,116 - INFO: Round 71: 30960099/30960099 AI 41957 AW 532308
2020-07-21 20:03:53,749 - INFO: Round 72: 30960099/30960099 AI 41971 AW 532512
2020-07-21 20:06:11,650 - INFO: Round 73: 30960099/30960099 AI 41984 AW 532822
2020-07-21 20:08:31,787 - INFO: Round 74: 30960099/30960099 AI 42015 AW 533280
2020-07-21 20:10:50,998 - INFO: Round 75: 30960099/30960099 AI 42082 AW 533840
2020-07-21 20:13:09,528 - INFO: Round 76: 30960099/30960099 AI 42146 AW 534820
2020-07-21 20:15:28,156 - INFO: Round 77: 30960099/30960099 AI 42228 AW 535958
2020-07-21 20:17:46,863 - INFO: Round 78: 30960099/30960099 AI 42276 AW 536592
2020-07-21 20:20:05,124 - INFO: Round 79: 30960099/30960099 AI 42313 AW 537282
2020-07-21 20:22:23,327 - INFO: Round 80: 30960099/30960099 AI 42378 AW 537910
2020-07-21 20:24:41,656 - INFO: Round 81: 30960099/30960099 AI 42405 AW 538412
2020-07-21 20:26:59,802 - INFO: Round 82: 30960099/30960099 AI 42426 AW 538698
2020-07-21 20:29:18,222 - INFO: Round 83: 30960099/30960099 AI 42463 AW 539278
2020-07-21 20:31:36,674 - INFO: Round 84: 30960099/30960099 AI 42522 AW 540100
2020-07-21 20:33:55,275 - INFO: Round 85: 30960099/30960099 AI 42561 AW 540928
2020-07-21 20:36:13,900 - INFO: Round 86: 30960099/30960099 AI 42597 AW 541548
2020-07-21 20:38:32,677 - INFO: Round 87: 30960099/30960099 AI 42609 AW 541738
2020-07-21 20:40:52,551 - INFO: Round 88: 30960099/30960099 AI 42613 AW 541832
2020-07-21 20:43:11,652 - INFO: Round 89: 30960099/30960099 AI 42617 AW 541920
2020-07-21 20:45:31,005 - INFO: Round 90: 30960099/30960099 AI 42617 AW 541920
2020-07-21 20:45:31,005 - INFO: No more reads found and terminated ...
2020-07-21 20:46:16,339 - INFO: Extending finished.

2020-07-21 20:46:16,986 - INFO: Separating filtered fastq file ...
2020-07-21 20:46:17,173 - INFO: Setting '-k 21,55,85,115'
2020-07-21 20:46:17,173 - INFO: Assembling using SPAdes ...
2020-07-21 20:46:17,227 - INFO: spades.py -t 4 -1 raw_mtgenome/filtered_1_paired.fq -2 raw_mtgenome/filtered_2_paired.fq --s1 raw_mtgenome/filtered_1_unpaired.fq --s2 raw_mtgenome/filtered_2_unpaired.fq -k 21,55,85,115 -o raw_mtgenome/filtered_spades
2020-07-21 20:46:35,198 - INFO: Insert size = 209.278, deviation = 59.7293, left quantile = 141, right quantile = 290
2020-07-21 20:46:35,198 - INFO: Assembling finished.

2020-07-21 20:46:36,956 - ERROR: Slimming raw_mtgenome/filtered_spades/K115/assembly_graph.fastg failed.
2020-07-21 20:46:37,729 - ERROR: Slimming raw_mtgenome/filtered_spades/K85/assembly_graph.fastg failed.
2020-07-21 20:46:38,478 - ERROR: Slimming raw_mtgenome/filtered_spades/K55/assembly_graph.fastg failed.

Total cost 13553.32 s
Thank you!

Broken assembly graph

Hi,
I tried to use my one seed/reference genome but I cant seem to keep it on running. I have copied my *.fasta file in SeedDatabase folder and change the command line for embplant_pt. Also my assembly produced 11 contigs in the file embplant_pt.K105.contigs.graph1.1.path_sequence.fasta. I am very new and using Bandage is quite confusing to me. Do you have any suggestions for me to complete and circularized my assembly?
Thank you for your time.

Speedup suggestion during initial FASTQ decompression

Thanks for developing GetOrganelle, it seems very complete and thorough. I am trying it for species of Ericaceae, hopefully it will handle the small repeats better than other software I tried in the past (any tips to improve these assemblies are welcome).

However, during my initial tests in a Mac I noticed it takes an excessive amount of time just to decompress the FASTQ files at the begginning (a file of ~5GB is taking more that 1.5 hours), my guess is that the combination of Mac's head + gunzip is the reason, I found that many of Mac's own standard programs are really slow compared to Linux's versions. My suggestion would be to use Python's own gzip library to decompress and compress reads more quickly, if not, the BBTools suite (https://jgi.doe.gov/data-and-tools/bbtools/) handles FASTQ files very fast as well, and a random subsampling could be performed with its program reformat.sh

Edgardo

the operation is killed before it finshes

Dear,
I have been trying to assembly plant mitochondria but the operation always gets killed.

Here I have attached a screenshot of the terminal

Thank you in advance.

How to use our own library instead of embplant_pt

Error during spades assembly

Hello,

I have been trying to run GetOrganelle and am running into an error in the Spades assembly -

'2018-04-13 14:11:36,749 - ERROR: Error in SPAdes:
== Error == system call for: "['/apps/spades/3.11.1/bin/spades', '/flush1/mcl300/Alangium/GetOrganelle/Alangium_output4/filtered_spades/K95/configs/config.info']" finished abnormally, err code: -8\n\n
2018-04-13 14:11:36,749 - ERROR: Assembling failed.

This error occurs in the final kmer assembly, no matter how many kmer values I try. For example, if I set kmer = 75,85,95, it will fail at 95. If I set k = 75, 85, it will fail at 85. If I set k=75, it won't run at all.

Here is the code I am using to run the software:

python /home/mcl300/GetOrganelle/get_organelle_reads.py \
-1 /home/mcl300/Alangium/13_4T_R1.fastq -2 /home/mcl300/Alangium/13_4T_R2.fastq \
-s /home/mcl300/Alangium/MG524996.fasta -w 103 -o Alangium_output4 \
-R 10 -F -k 75,85,95 -P 0 --out-per-round --no-remove-duplicates --verbose --spades-options "--memory 1000 --threads 10 --phred-offset 33"

Any help would be appreciated.

Cheers,
Todd

WARNING: Please check the final result to confirm whether they are simply flip-flop configurations!

I'm trying to assemble the chloroplast of a prunus.
I have set a prunus_cp file in GetOrganelle/Library/SeqReference
and generated the corresponding blast db (makeblastdb in /gpfs/home/ag/GetOrganelle/Library/NotationReference
But i'm facing this error at the desentangling step :
Disentangling failed: list index out of range
Here is the full log :
get_org.log.txt.zip

On the interpretation of visualized *.fastg file

Hi,@Kinggerm!
I used Getorganelle to assemble Chloroplast.First time,I used total 1G data to assemble,which means about 500M per end with below code.

head -n 4444444 xx_L1_1.rd.fq >1.rd.fq
head -n 4444444 xx_L1_2.rd.fq >2.rd.fq
… #There are three lanes totally I used.
get_organelle_from_reads.py -1 1.rd.fq -2 2.rd.fq -o plastome_output -R 15 -k 21,45,65,85,105 -F embplant_pt -t 16"

The result is perfect.

Then I noticed that you advice to use 1G per end to assemble chloroplast.So I extracted more data.However,in this time,the extracting code is:

head -n 8888888 xx_L1_1.rd.fq >1.rd.fq
head -n 8888888 xx_L1_2.rd.fq >2.rd.fq

With the same codes in other steps,I got the result with a special low-depth node in chloroplast loop.I blasted the node in NCBI,and found it is a segment of mitochondria.

Then I thought it may be the result of 'head',so I used seqtk to extract.

seqtk sample -s11 xx_L1_1.rd.fq 2222222 >xx.1.1G.rd.fq
seqtk sample -s11 xx_L1_2.rd.fq 2222222 >xx.2.1G.rd.fq

The result became like this:

I had blasted two low-depth node ,they are just mitochondiral segments.

In one words,I used less data assemble successfully,but failed with more data.So is it normal to get a chloroplast with mitochondria segments?How can I get a pure chloroplast loop?Or it is ok to remove the node in bandage?

Thank you!

Best wishes

Minor comments on the installation instructions

Hi @Kinggerm

we are currently working on a benchmarking of chloroplast assembly tools (see https://github.com/chloroExtractorTeam/benchmark). In this context, I installed GetOrganelle on a fresh installation of Ubuntu 18.04.2 and noticed a few things you might want to add to your installation instructions:

pip and git are not installed by default
the GetOrganellePATH directory has to be created first.
it would be nice to have a test dataset, so I can check the functionality after installation

Best,

Niklas

KeyError: 'animal_mt'

Hi, @Kinggerm,

I am trying to assemble the mitochondrion from my termite using the following code:

get_organelle_from_reads.py -1 CIVT039_S65_R1_001_val_1.fq.gz -2 CIVT039_S65_R2_001_val_2.fq.gz -o CIVT039 -s Astalotermes_genome.fasta.txt --genes Astalotermes_gene_features_sequence.txt -R 3 -k 21,45,65,85,105 -F animal_mt

Using this configuration:

GetOrganelle v1.6.2

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.7.1 (default, Dec 14 2018, 19:28:38) [GCC 7.3.0]
Python libs: numpy 1.16.4; sympy 1.4; scipy 1.3.0
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30

However, after the assembly step using SPAdes and the slimming of assembly graphs, I get the following:

2019-07-02 14:51:57,241 - INFO: Extracting animal_mt from the assemblies ...
2019-07-02 14:51:57,243 - INFO: Disentangling CIVT039_S65_R1_001_val_1_output/filtered_spades/K105/assembly_graph.fastg.extend-Astalotermes_gene_features_sequence.txt.fastg as a circular genome ...
2019-07-02 14:51:57,249 - ERROR:
Traceback (most recent call last):
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3340, in extract_organelle_genome
temp_graph=graph_temp_file)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3302, in disentangle_assembly
acyclic_allowed_in=here_acyclic_allowed, verbose_in=here_verbose, in_temp_graph=temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/pipe_control_func.py", line 85, in func_modified
r = func(*args, **kwargs)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3189, in disentangle_inside
temp_graph=in_temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1769, in find_target_graph
self.parse_tab_file(tab_file, mode=mode, type_factor=type_factor, log_handler=log_handler)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1250, in parse_tab_file
if len(self.tagged_vertices[mode]) == 0:
KeyError: 'animal_mt'
2019-07-02 14:51:57,254 - ERROR:
Traceback (most recent call last):
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3340, in extract_organelle_genome
temp_graph=graph_temp_file)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3302, in disentangle_assembly
acyclic_allowed_in=here_acyclic_allowed, verbose_in=here_verbose, in_temp_graph=temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/pipe_control_func.py", line 85, in func_modified
r = func(*args, **kwargs)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3189, in disentangle_inside
temp_graph=in_temp_graph)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1769, in find_target_graph
self.parse_tab_file(tab_file, mode=mode, type_factor=type_factor, log_handler=log_handler)
File "/home/ulb/ebe/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/GetOrganelleLib/assembly_parser.py", line 1250, in parse_tab_file
if len(self.tagged_vertices[mode]) == 0:
KeyError: 'animal_mt'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3803, in main
options=options)
File "/home/users/s/i/sihellem/miniconda3/lib/python3.7/site-packages/GetOrganelle-1.6.2-py3.7.egg/EGG-INFO/scripts/get_organelle_from_reads.py", line 3353, in extract_organelle_genome
sys.exit()
SystemExit

Total cost 317.57 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

Do you have any idea of what's happening here?

Thanks a lot in advance!

Differences of complete.1.path_ and complete.2.path_ output files

I could get final files *.complete.graph1.1.path_sequence and *.complete.graph1.2.paht_sequence fasta files at the end.

I want to know the differences between these output files.
I think the bases are the same (maybe almost the same??).

Thank you.

Any additional hints to reduce memory usage?

GetOrganelle v1.6.2e

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.6.8 (default, Oct 7 2019, 12:59:55) [GCC 8.3.0]
Python libs: numpy 1.17.4; sympy 1.4; scipy 1.3.2; psutil 5.4.2
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30; Bandage 0.8.1
./get_organelle_from_reads.py -1 /home/xub/host/opt/sra_processor/output/SRR7002309_pass_1.fastq.gz -2 /home/xub/host/opt/sra_processor/output/SRR7002309_pass_2.fastq.gz -o /home/xub/get0rganelle_output/ta_mitochondria_output -k 21,45,65,85,105 --disentangle-time-limit=1200 -R 500 -P 1000000 -F embplant_mt --memory-save

2019-12-21 12:38:13,652 - WARNING: removing duplicates was inactive, so that the pre-grouping was disabled.
2019-12-21 12:38:13,653 - INFO: Pre-reading fastq ...
2019-12-21 12:38:13,654 - INFO: Estimating reads to use ... (to skip, set '--reduce-reads-for-coverage inf')
2019-12-21 12:38:15,334 - INFO: Tasting 100000+100000 reads ...
2019-12-21 12:38:37,949 - INFO: Tasting 500000+500000 reads ...
2019-12-21 12:39:26,174 - INFO: Tasting 2500000+2500000 reads ...
2019-12-21 12:43:41,578 - INFO: Estimating reads to use finished.
2019-12-21 12:43:41,580 - INFO: Unzipping reads file: /home/xub/host/opt/sra_processor/output/SRR7002309_pass_1.fastq.gz (7112302855 bytes)
2019-12-21 12:50:01,188 - INFO: Unzipping reads file: /home/xub/host/opt/sra_processor/output/SRR7002309_pass_2.fastq.gz (7314668784 bytes)
2019-12-21 12:56:30,094 - INFO: Counting read qualities ...
2019-12-21 12:56:30,798 - INFO: Identified quality encoding format = Sanger
2019-12-21 12:56:30,800 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2019-12-21 12:56:30,934 - INFO: Mean error rate = 0.0047
2019-12-21 12:56:30,935 - INFO: Counting read lengths ...
2019-12-21 13:07:44,830 - INFO: Mean = 158.4 bp, maximum = 160 bp.
2019-12-21 13:07:44,831 - INFO: Reads used = 75000000+75000000
2019-12-21 13:07:44,831 - INFO: Pre-reading fastq finished.

2019-12-21 13:07:44,831 - INFO: Making seed reads ...
2019-12-21 13:07:44,832 - INFO: Seed bowtie2 index existed!
2019-12-21 13:07:44,832 - INFO: Mapping reads to seed bowtie2 index ...
2019-12-21 14:19:30,064 - INFO: Mapping finished.
2019-12-21 14:19:30,065 - INFO: Seed reads made: /home/xub/get0rganelle_output/ta_mitochondria_output/seed/embplant_mt.initial.fq (42323924 bytes)
2019-12-21 14:19:30,065 - INFO: Making seed reads finished.

2019-12-21 14:19:30,066 - INFO: Checking seed reads and parameters ...
2019-12-21 14:19:30,066 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2019-12-21 14:19:30,066 - INFO: If the result graph is not a circular organelle genome,
2019-12-21 14:19:30,066 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2019-12-21 14:19:50,995 - INFO: Pre-assembling mapped reads ...
2019-12-21 14:20:27,164 - INFO: Pre-assembling mapped reads finished.
2019-12-21 14:20:27,164 - INFO: Estimated embplant_mt-hitting base-coverage = 185.92
2019-12-21 14:20:27,165 - INFO: Estimated word size(s): 98
2019-12-21 14:20:27,165 - INFO: Setting '-w 98'
2019-12-21 14:20:27,165 - INFO: Setting '--max-extending-len inf'
2019-12-21 14:20:27,443 - INFO: Checking seed reads and parameters finished.

2019-12-21 14:20:27,443 - INFO: Making read index ...
2019-12-21 15:03:48,887 - INFO: Mem 17.049 G, 149411106 reads
2019-12-21 15:04:03,093 - INFO: Making read index finished.

2019-12-21 15:04:03,093 - INFO: Extending ...
2019-12-21 15:04:03,093 - INFO: Adding initial words ...
2019-12-21 15:04:16,654 - INFO: AW 3772354
2019-12-21 16:04:24,226 - INFO: Round 1: 149411106/149411106 AI 2996481 AW 28419298 Mem 5.646
2019-12-21 17:03:34,772 - INFO: Round 2: 149411106/149411106 AI 6364512 AW 73504374 Mem 13.613
2019-12-21 18:06:20,553 - INFO: Round 3: 149411106/149411106 AI 12032426 AW 149532000 Mem 20.882
2019-12-21 18:33:23,886 - ERROR:
Traceback (most recent call last):
File "./get_organelle_from_reads.py", line 3705, in main
echo_step=echo_step, log_handler=log_handler)
File "./get_organelle_from_reads.py", line 2362, in extending_no_lim
accepted_words.add(this_seq[i:i + word_size])
MemoryError

Total cost 21311.26 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

WARNING: Separating filtered fastq file failed

Hello,
I am trying to run GetOrganelle for assembling chloroplast genome and I am getting error

WARNING: Separating filtered fastq file failed with unknown error: /media/anu/50572A1F605A32C7/getorganelle/GetOrganelle/Utilities/get_pair_reads.py 300R_cp_no_ref/filtered_1.fq 300R_cp_no_ref/filtered_2.fq

The log file is like this:

GetOrganelle v1.5.1c

gets organelle reads and genomes from genome skimming data by extending.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 2.7.6 (default, Nov 13 2018, 12:45:42)
[GCC 4.8.4]
get_organelle_reads.py -1 /media/anu/Seagate_Drive_Anu/Evolvulus/illumina/R1_mapped.fastq -2 /media/anu/Seagate_Drive_Anu/Evolvulus/illumina/R2_mapped.fastq -o 300R_cp_no_ref -R 15 -k 45,65,85,105,115 -F plant_cp

2019-04-03 16:50:46,052 - INFO: Pre-reading fastq ...
2019-04-03 16:50:46,052 - INFO: Counting read qualities ...
2019-04-03 16:54:13,727 - INFO: Identified quality encoding format = Illumina 1.8+
2019-04-03 16:54:13,940 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2019-04-03 16:54:20,954 - INFO: Mean error rate = 0.0025
2019-04-03 16:54:21,045 - INFO: Counting read lengths ...
2019-04-03 16:57:24,508 - INFO: Mean = 149.0 bp, maximum = 150 bp.
2019-04-03 16:57:24,508 - INFO: Reads used = 25768336
2019-04-03 16:57:24,508 - INFO: Pre-reading fastq finished.

2019-04-03 16:57:24,508 - INFO: Making seed reads ...
2019-04-03 16:57:25,039 - INFO: Bowtie2 index existed!
2019-04-03 16:57:25,039 - INFO: Mapping reads to seed - bowtie2 index ...
2019-04-03 17:34:37,569 - INFO: Mapping finished.
2019-04-03 17:34:37,570 - INFO: Seed reads made: 300R_cp_no_ref/Initial.mapped.fq (3232.00 M)
2019-04-03 17:34:37,570 - INFO: Making seed reads finished.

2019-04-03 17:34:37,570 - INFO: Checking seed reads and parameters ...
2019-04-03 17:41:05,985 - INFO: Estimated plant_cp base-coverage = 34627.0
2019-04-03 17:41:06,072 - INFO: Setting '-w 111'
2019-04-03 17:41:06,072 - INFO: The automatically-estimated word size does not ensure the best choice.
2019-04-03 17:41:06,073 - INFO: If the result graph is not a circular organelle genome,
2019-04-03 17:41:06,073 - INFO: you could adjust the word size for another new run.
2019-04-03 17:41:06,078 - INFO: Checking seed reads and parameters finished.

2019-04-03 17:41:06,078 - INFO: Making read index ...
2019-04-03 17:45:59,244 - INFO: Mem 2.588 G, 4606811 candidates in all 25768336 reads
2019-04-03 17:45:59,816 - INFO: Pre-grouping reads ...
2019-04-03 17:45:59,817 - INFO: Setting '--pre-w 111'
2019-04-03 17:46:01,212 - INFO: Mem 2.337 G, 200000/404776 used/duplicated
2019-04-03 17:46:07,653 - INFO: Mem 2.504 G, 788 groups made.
2019-04-03 17:46:09,269 - INFO: Making read index finished.

2019-04-03 17:46:09,288 - INFO: Extending ...
2019-04-03 17:46:09,298 - INFO: Adding initial words ...
2019-04-03 17:52:22,257 - INFO: AW 51136114
2019-04-03 20:05:17,481 - INFO: Round 1: 4606811/4606811 AI 3378939 AW 75595392 Mem 14.316
2019-04-03 20:05:43,104 - INFO: Round 2: 4606811/4606811 AI 3615311 AW 80625262 Mem 14.483
2019-04-03 20:05:59,645 - INFO: Round 3: 4606811/4606811 AI 3637147 AW 81114066 Mem 14.461
2019-04-03 20:06:13,604 - INFO: Round 4: 4606811/4606811 AI 3639023 AW 81150346 Mem 14.451
2019-04-03 20:06:27,687 - INFO: Round 5: 4606811/4606811 AI 3639076 AW 81151600 Mem 14.452
2019-04-03 20:06:41,637 - INFO: Round 6: 4606811/4606811 AI 3639201 AW 81153148 Mem 14.424
2019-04-03 20:06:55,178 - INFO: Round 7: 4606811/4606811 AI 3639299 AW 81153852 Mem 14.424
2019-04-03 20:07:08,594 - INFO: Round 8: 4606811/4606811 AI 3639311 AW 81154050 Mem 14.425
2019-04-03 20:07:21,988 - INFO: Round 9: 4606811/4606811 AI 3639319 AW 81154182 Mem 14.425
2019-04-03 20:07:35,378 - INFO: Round 10: 4606811/4606811 AI 3639319 AW 81154182 Mem 14.392
2019-04-03 20:07:35,414 - INFO: No more reads found and terminated ...
2019-04-03 21:28:07,622 - INFO: Extending finished.

2019-04-03 21:28:07,808 - INFO: Separating filtered fastq file ...
2019-04-03 21:28:09,036 - WARNING: Separating filtered fastq file failed with unknown error: /media/anu/50572A1F605A32C7/getorganelle/GetOrganelle/Utilities/get_pair_reads.py 300R_cp_no_ref/filtered_1.fq 300R_cp_no_ref/filtered_2.fq
2019-04-03 21:28:09,105 - INFO: Setting '-k 45,65,85,105,115'
2019-04-03 21:28:09,152 - INFO: Assembling using SPAdes ...
2019-04-04 02:08:03,068 - INFO: Assembling finished.

2019-04-04 02:08:03,600 - INFO: Slimming and disentangling graph ...
2019-04-04 02:08:08,543 - INFO: Slimming 300R_cp_no_ref/filtered_spades/K115/assembly_graph.fastg finished!
2019-04-04 02:08:08,552 - INFO: Disentangling failed: list index out of range
2019-04-04 02:08:08,758 - INFO: Slimming 300R_cp_no_ref/filtered_spades/K105/assembly_graph.fastg finished!
2019-04-04 02:08:08,761 - INFO: Disentangling failed: list index out of range
2019-04-04 02:08:08,956 - INFO: Slimming 300R_cp_no_ref/filtered_spades/K85/assembly_graph.fastg finished!
2019-04-04 02:08:08,957 - INFO: Disentangling failed: list index out of range
2019-04-04 02:08:09,184 - INFO: Slimming 300R_cp_no_ref/filtered_spades/K65/assembly_graph.fastg finished!
2019-04-04 02:08:09,187 - INFO: Disentangling failed: list index out of range
2019-04-04 02:08:09,379 - INFO: Slimming 300R_cp_no_ref/filtered_spades/K45/assembly_graph.fastg finished!
2019-04-04 02:08:09,386 - INFO: Disentangling failed: list index out of range
2019-04-04 02:08:09,389 - INFO: Please ...
2019-04-04 02:08:09,389 - INFO: load the graph file: 300R_cp_no_ref/filtered_spades/assembly_graph.fastg
2019-04-04 02:08:09,393 - INFO: visualize and export your result in Bandage.
2019-04-04 02:08:09,393 - INFO: If you have questions for us, please provide us with the get_org.log.txt file and the graph in the format you like!

Total cost 33445.38 s
Thank you!

Can u Plz suggest me how to correct this error?

How can I choose the assembled sequences

Hi Jianjun,

I have used GetOrganelle to assemble the cp genome. Reads were generated by sequencing genomic DNA with Hiseq2500 (150bp paired reads).
After running the GetOrganelle, I got two fasta files for each sample. For example file name and sequence heads:
1-1_embplant_pt.K105.complete.graph1.1.path_sequence.fasta:

32639050_32105184_32124232-,32481135-,32384871-,32481135+(circular)

1-1_embplant_pt.K105.complete.graph1.2.path_sequence.fasta:

32639050_32105184_32124232-,32481135-,32384871+,32481135+(circular)
However, the two sequences are very different in some regions. The rest seems to be completely identical.
Which sequence should be used for further analysis? Which is more accurate?
Thank you so much.

Best,
Lingyun

Reg: Mitochondrial Genome Assembly

Hi!

We have done an assembly of the mitochondria, but the Bandage plot looks like the following:

Can you suggest a way to filter the same? I did go through your youtube video, wherein you show the duplicate+depth segregation, but I'm unsure for this assembly.

Interpretation of .fastg file and advice to simplify

get_org.log.txt

Good day,

I have assembled a chloroplast genome using GetOrganelle, and would like your advice on how to simplify the graph.

I have watched the following youtube video, but I don't understand what is being done and why:
https://www.youtube.com/watch?v=cXUV7k-F26w&ab_channel=Wen-BinYu

I have attached both the log file as well as the Bandage output.

Thank you for your time.

Regards,
Allison

How to use the scipt "summary_get_organelle_output.py?

I would like to asked how to use the script of "summary_get_organelle_output.py . I don't know the input file. In addition, I would like to asked what was the meaning of "Aligned: 375.33±66.39 (375.33±66.39)" , the one of data value come from the script: evaluate_assembly_using_mapping.py.Thank you very much!

GetOrganelle Flowchart

mitochondria assembly with pacbio

I we're trying to assemble the sequences using pacbio data and I've ran this twice; one with the short reads and another will the pacbio reads.

without short reads:

GetOrganelle v1.6.2b

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 02:32:25)  [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Python libs: numpy 1.14.3; sympy 1.3; scipy 1.2.0; psutil 5.4.8
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
./GetOrganelle/get_organelle_from_reads.py -u ./pacbio/m54048_180110_204750.fq ./pacbio/m54048_180117_052827.fq ./pacbio/m54048_180117_153809.fq ./pacbio/m54048_180121_041959.fq ./pacbio/m54048_180121_142957.fq ./pacbio/m54048_180122_105730.fq ./pacbio/m54048_180122_210722.fq ./pacbio/m54048_180124_232643.fq ./pacbio/m54048_180125_093419.fq ./pacbio/m54048_180125_194409.fq -F embplant_mt -R 50 --memory-save -k 19,21,23,25,27,61,111 -s ./mitochondrion.fasta -o mitochondrion_pacbio_jul_16_2019

2019-07-17 23:21:10,261 - INFO: Pre-reading fastq ...
2019-07-17 23:21:10,262 - INFO: Estimating reads to use ...
2019-07-17 23:21:11,462 - INFO: Estimating reads to use finished.
2019-07-17 23:21:46,944 - INFO: Counting read qualities ...
2019-07-17 23:21:51,742 - INFO: Identified quality encoding format = Sanger
2019-07-17 23:21:51,823 - INFO: Resetting '--min-quality-score 0'
2019-07-17 23:21:53,259 - INFO: Mean error rate = 1.0
2019-07-17 23:21:53,279 - INFO: Counting read lengths ...
2019-07-17 23:21:55,899 - INFO: Mean = 11859.6 bp, maximum = 65068 bp.
2019-07-17 23:21:55,900 - INFO: Reads used = 139991
2019-07-17 23:21:55,900 - INFO: Pre-reading fastq finished.

2019-07-17 23:21:55,900 - INFO: Making seed reads ...
2019-07-17 23:21:56,074 - INFO: Making seed - bowtie2 index ...
2019-07-17 23:21:56,744 - INFO: Making seed - bowtie2 index finished.
2019-07-17 23:21:56,745 - INFO: Mapping reads to seed bowtie2 index ...
2019-07-18 04:48:18,842 - INFO: Mapping finished.
2019-07-18 04:48:18,843 - INFO: Seed reads made: mitochondrion_pinta_pacbio_jul_16_2019/seed/embplant_mt.initial.fq (9318040 bytes)
2019-07-18 04:48:18,844 - INFO: Making seed reads finished.

2019-07-18 04:48:18,844 - INFO: Checking seed reads and parameters ...
2019-07-18 04:48:18,844 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2019-07-18 04:48:18,844 - INFO: If the result graph is not a circular organelle genome, 
2019-07-18 04:48:18,845 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2019-07-18 04:48:29,498 - INFO: Pre-assembling mapped reads ...
2019-07-18 06:48:39,180 - WARNING: Pre-assembling failed. The estimations for embplant_mt-hitting base-coverage and word size may be misleading.
2019-07-18 06:48:40,499 - INFO: Estimated embplant_mt-hitting base-coverage = 329.92
2019-07-18 06:48:48,591 - ERROR: 
Traceback (most recent call last):
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3636, in main
    resume=resume, verbose_log=verb_log, zip_files=options.zip_files)
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 1459, in check_parameters
    wc_bc_ratio_constant=wc_bc_ratio_constant, organelle_type=organelle_types[go_type])
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 1091, in estimate_word_size
    estimated_word_size = int(read_length * (1 - word_cov / base_cov)) + 1
ValueError: cannot convert float NaN to integer

Total cost 26859.11 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

with short reads:


GetOrganelle v1.6.2b

get_organelle_from_reads.py assembles organelle genomes from genome skimming data.
Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 02:32:25)  [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Python libs: numpy 1.14.3; sympy 1.3; scipy 1.2.0; psutil 5.4.8
Dependencies: Bowtie2 2.3.5.1; SPAdes 3.13.0; Blast 2.2.30
/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py -1 ./HA1_DSW64714-V_HT2GMCCXY_L4_1.fq.gz ./HA1_DSW64714-V_HT2GMCCXY_L5_1.fq.gz ./HA1_DSW64714-V_HT2GMCCXY_L6_1.fq.gz ./HA1_DSW64714-V_HT2GMCCXY_L7_1.fq.gz -2 ./HA1_DSW64714-V_HT2GMCCXY_L4_2.fq.gz ./HA1_DSW64714-V_HT2GMCCXY_L5_2.fq.gz ./HA1_DSW64714-V_HT2GMCCXY_L6_2.fq.gz ./HA1_DSW64714-V_HT2GMCCXY_L7_2.fq.gz -u ./pacbio/m54048_180110_204750.fq ./pacbio/m54048_180117_052827.fq ./pacbio/m54048_180117_153809.fq ./pacbio/m54048_180121_041959.fq ./pacbio/m54048_180121_142957.fq ./pacbio/m54048_180122_105730.fq ./pacbio/m54048_180122_210722.fq ./pacbio/m54048_180124_232643.fq ./pacbio/m54048_180125_093419.fq ./pacbio/m54048_180125_194409.fq -F embplant_mt -R 50 --memory-save -k 19,21,23,25,27,61,111 -s ./mitochondrion.fasta -o mitochondrion_pacbio_jul_16_2019_with_short_reads

2019-07-17 14:24:52,985 - INFO: Pre-reading fastq ...
2019-07-17 14:24:52,986 - INFO: Estimating reads to use ...
2019-07-17 14:24:54,407 - INFO: Tasting 100000+100000+100000 reads ...
2019-07-17 20:52:05,080 - INFO: Estimating reads to use finished.
2019-07-17 20:52:05,081 - INFO: Unzipping reads file: ./Pinta/HA1_DSW64714-V_HT2GMCCXY_L4_1.fq.gz (7417399283 bytes)
2019-07-17 20:53:23,926 - INFO: Unzipping reads file: ./Pinta/HA1_DSW64714-V_HT2GMCCXY_L4_2.fq.gz (8342958686 bytes)
2019-07-17 20:54:54,201 - INFO: Counting read qualities ...
2019-07-17 20:55:00,871 - INFO: Identified quality encoding format = Illumina 1.8+
2019-07-17 20:55:00,954 - INFO: Resetting '--min-quality-score 0'
2019-07-17 20:55:03,094 - INFO: Mean error rate = 0.9761
2019-07-17 20:55:03,117 - INFO: Counting read lengths ...
2019-07-17 20:56:43,024 - INFO: Mean = 160.7 bp, maximum = 61722 bp.
2019-07-17 20:56:43,024 - INFO: Reads used = 15726496+15726496+27774
2019-07-17 20:56:43,024 - INFO: Pre-reading fastq finished.

2019-07-17 20:56:43,025 - INFO: Making seed reads ...
2019-07-17 20:56:43,059 - INFO: Making seed - bowtie2 index ...
2019-07-17 20:56:43,687 - INFO: Making seed - bowtie2 index finished.
2019-07-17 20:56:43,688 - INFO: Mapping reads to seed bowtie2 index ...
2019-07-17 22:15:19,063 - INFO: Mapping finished.
2019-07-17 22:15:19,065 - INFO: Seed reads made: mitochondrion_pinta_pacbio_jul_16_2019_with_short_reads/seed/embplant_mt.initial.fq (754284740 bytes)
2019-07-17 22:15:19,065 - INFO: Making seed reads finished.

2019-07-17 22:15:19,065 - INFO: Checking seed reads and parameters ...
2019-07-17 22:15:19,066 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2019-07-17 22:15:19,066 - INFO: If the result graph is not a circular organelle genome, 
2019-07-17 22:15:19,066 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2019-07-17 22:17:02,294 - INFO: Pre-assembling mapped reads ...
2019-07-17 22:22:28,112 - INFO: Pre-assembling mapped reads finished.
2019-07-17 22:22:28,112 - INFO: Estimated embplant_mt-hitting base-coverage = 1084.55
2019-07-17 22:22:28,112 - INFO: Reads reduced to = 7250236+7250236+12804
2019-07-17 22:22:28,112 - INFO: Adjusting expected embplant_mt base coverage to 500.00
2019-07-17 22:22:28,114 - INFO: Estimated word size(s): 120
2019-07-17 22:22:28,114 - INFO: Setting '-w 120'
2019-07-17 22:22:28,114 - INFO: Setting '--max-extending-len inf'
2019-07-17 22:22:32,109 - INFO: Checking seed reads and parameters finished.

2019-07-17 22:22:32,110 - INFO: Making read index ...
2019-07-17 22:23:10,076 - INFO: For mitochondrion_pinta_pacbio_jul_16_2019_with_short_reads/1-HA1_DSW64714-V_HT2GMCCXY_L4_1.fq.gz.fastq, only top 7250236 reads are used in downstream analysis.
2019-07-17 22:23:39,306 - INFO: For mitochondrion_pinta_pacbio_jul_16_2019_with_short_reads/2-HA1_DSW64714-V_HT2GMCCXY_L4_2.fq.gz.fastq, only top 7250236 reads are used in downstream analysis.
2019-07-17 22:23:40,034 - INFO: For mitochondrion_pinta_pacbio_jul_16_2019_with_short_reads/3-m54048_180110_204750.fq, only top 12804 reads are used in downstream analysis.
2019-07-17 22:24:10,217 - INFO: Mem 1.836 G, 14513259 reads
2019-07-17 22:24:11,278 - INFO: Making read index finished.

2019-07-17 22:24:11,278 - INFO: Extending ...
2019-07-17 22:24:11,278 - INFO: Adding initial words ...
2019-07-17 22:25:10,729 - INFO: AW 14208410
2019-07-17 22:27:11,914 - INFO: Round 1: 14513259/14513259 AI 1854057 AW 15495760 Mem 3.443
2019-07-17 22:28:40,790 - INFO: Round 2: 14513259/14513259 AI 2378131 AW 16148864 Mem 3.568
2019-07-17 22:30:07,553 - INFO: Round 3: 14513259/14513259 AI 2505435 AW 16338056 Mem 3.603
2019-07-17 22:31:32,237 - INFO: Round 4: 14513259/14513259 AI 2518460 AW 16387532 Mem 3.611
2019-07-17 22:32:56,658 - INFO: Round 5: 14513259/14513259 AI 2525373 AW 16415728 Mem 3.616
2019-07-17 22:34:20,164 - INFO: Round 6: 14513259/14513259 AI 2530083 AW 16436008 Mem 3.62
2019-07-17 22:35:45,335 - INFO: Round 7: 14513259/14513259 AI 2533065 AW 16449790 Mem 3.622
2019-07-17 22:37:11,266 - INFO: Round 8: 14513259/14513259 AI 2535577 AW 16460300 Mem 3.624
2019-07-17 22:38:33,329 - INFO: Round 9: 14513259/14513259 AI 2537491 AW 16469288 Mem 3.626
2019-07-17 22:39:56,800 - INFO: Round 10: 14513259/14513259 AI 2539066 AW 16475908 Mem 3.627
2019-07-17 22:41:20,945 - INFO: Round 11: 14513259/14513259 AI 2540401 AW 16481888 Mem 3.628
2019-07-17 22:42:44,312 - INFO: Round 12: 14513259/14513259 AI 2541787 AW 16487286 Mem 3.629
2019-07-17 22:44:07,382 - INFO: Round 13: 14513259/14513259 AI 2543128 AW 16492716 Mem 3.63
2019-07-17 22:45:31,855 - INFO: Round 14: 14513259/14513259 AI 2544382 AW 16497580 Mem 3.631
2019-07-17 22:46:55,018 - INFO: Round 15: 14513259/14513259 AI 2545237 AW 16501210 Mem 3.631
2019-07-17 22:48:15,244 - INFO: Round 16: 14513259/14513259 AI 2545754 AW 16503414 Mem 3.632
2019-07-17 22:49:41,764 - INFO: Round 17: 14513259/14513259 AI 2545877 AW 16504016 Mem 3.632
2019-07-17 22:51:02,758 - INFO: Round 18: 14513259/14513259 AI 2545925 AW 16504570 Mem 3.632
2019-07-17 22:52:26,045 - INFO: Round 19: 14513259/14513259 AI 2545956 AW 16504756 Mem 3.632
2019-07-17 22:53:45,538 - INFO: Round 20: 14513259/14513259 AI 2545989 AW 16505104 Mem 3.632
2019-07-17 22:55:04,942 - INFO: Round 21: 14513259/14513259 AI 2546001 AW 16505246 Mem 3.632
2019-07-17 22:56:23,664 - INFO: Round 22: 14513259/14513259 AI 2546005 AW 16505294 Mem 3.632
2019-07-17 22:57:45,126 - INFO: Round 23: 14513259/14513259 AI 2546005 AW 16505294 Mem 3.632
2019-07-17 22:57:45,127 - INFO: No more reads found and terminated ...
2019-07-17 22:58:31,637 - INFO: Extending finished.

2019-07-17 22:58:32,672 - INFO: Separating filtered fastq file ... 
2019-07-17 22:58:53,638 - INFO: Setting '-k 21,23,25,27,61,111'
2019-07-17 22:58:53,639 - INFO: Assembling using SPAdes ...
2019-07-17 23:21:01,904 - ERROR: Error in SPAdes: 
== Error ==  system call for: "['/home/[email protected]/Hagop/GetOrganelle/GetOrganelleDep/linux/SPAdes/bin/spades-core', '/home/[email protected]/Hagop/mitochondrion_pinta_pacbio_jul_16_2019_with_short_reads/filtered_spades/K21/configs/config.info']" finished abnormally, err code: 255


2019-07-17 23:21:01,904 - ERROR: Assembling failed.

Total cost 32169.49 s
Thank you!

Error correction and assembling warnings

I tried to assemble chloroplast using:
get_organelle_reads.py -1 SRR6175507_1.fastq -2 SRR6175507_2.fastq -s Ref.fasta -o SRR6175507 -R 40 -k 75,85,95,105 --spades-options --careful
I got some warnings at the assembly step and I don't know whether these will obtain a wrong assembly results or not. Below some warnings of the file spades.log:

======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:

0:01:08.830 316M / 3G WARN General (kmer_coverage_model.cpp : 218) Too many erroneous kmers, the estimates might be unreliable
0:01:32.553 312M / 3G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 12
0:01:32.555 312M / 3G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 12
0:00:56.624 320M / 3G WARN General (kmer_coverage_model.cpp : 327) Valley value was estimated improperly, reset to 3
0:00:56.626 320M / 3G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 3
0:00:51.189 328M / 3G WARN General (kmer_coverage_model.cpp : 366) Failed to determine erroneous kmer threshold. Threshold set to: 63
0:01:36.512 448M / 3G WARN General (simplification.cpp : 479) The determined erroneous connection coverage threshold may be determined improperly

I have seet you the intact log file.

Besides, I have some single-end data to assemble, but I don't know how to deal with it using this pipeline. Can you tell me something about it?

thanks for your help.

what doesn mean by -p?

Hi,
I would like to know what does -p 1000000 stands for in the command? and Kmer value is important in the commands??

get_organelle_from_reads.py -1 sample_1.fq -2 sample_2.fq -o mitochondria_output -R 50 -k 21,45,65,85,105 -P 1000000 -F embplant_mt

Slimming fails

Can I please have some help with an error I am getting. I installed GetOrganelle on ubuntu. For some reason the runs do not complete with an error appearing that says that slimming has failed. I have pasted the log below. Any help with resolving this issue would be much appreciated.

Python 3.7.0 (default, Jun 28 2018, 13:15:42) [GCC 7.2.0]
PYTHON LIBS: GetOrganelleLib 1.7.1a; numpy 1.19.1; sympy 1.6.2; scipy 1.5.2
DEPENDENCIES: Bowtie2 2.3.4.1; SPAdes 3.11.1; Blast 2.6.0
LABEL DB: embplant_pt 0.0.0; embplant_mt 0.0.0
WORKING DIR: /mnt/j/BGI shotgun sequence data August 13th 2020/Kurobe-17 Higashiakaishi
/home/james/miniconda3/bin/get_organelle_from_reads.py -1 V300068204_L2_THUtakRBAAB-608_1.fq -2 V300068204_L2_THUtakRBAAB-608_2.fq -s KX832627.fasta -o Kurobe17_output -R 15 -k 21,45,65,85,105 -F embplant_pt

2020-08-19 08:38:24,198 - INFO: Pre-reading fastq ...
2020-08-19 08:38:24,200 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-08-19 08:38:24,764 - INFO: Tasting 100000+100000 reads ...
2020-08-19 08:38:35,643 - INFO: Estimating reads to use finished.
2020-08-19 08:39:31,329 - INFO: Counting read qualities ...
2020-08-19 08:39:31,521 - INFO: Identified quality encoding format = Sanger
2020-08-19 08:39:31,523 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2020-08-19 08:39:31,601 - INFO: Mean error rate = 0.0029
2020-08-19 08:39:31,603 - INFO: Counting read lengths ...
2020-08-19 08:39:47,957 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2020-08-19 08:39:47,958 - INFO: Reads used = 4114149+4114149
2020-08-19 08:39:47,958 - INFO: Pre-reading fastq finished.

2020-08-19 08:39:47,959 - INFO: Making seed reads ...
2020-08-19 08:39:48,137 - INFO: Seed bowtie2 index existed!
2020-08-19 08:39:48,140 - INFO: Mapping reads to seed bowtie2 index ...
2020-08-19 08:41:11,502 - INFO: Mapping finished.
2020-08-19 08:41:11,503 - INFO: Seed reads made: Kurobe17_output/seed/embplant_pt.initial.fq (31862520 bytes)
2020-08-19 08:41:11,504 - INFO: Making seed reads finished.

2020-08-19 08:41:11,505 - INFO: Checking seed reads and parameters ...
2020-08-19 08:41:11,505 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2020-08-19 08:41:11,506 - INFO: If the result graph is not a circular organelle genome,
2020-08-19 08:41:11,506 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2020-08-19 08:41:16,591 - INFO: Pre-assembling mapped reads ...
2020-08-19 08:43:08,014 - WARNING: Pre-assembling failed. The estimations for embplant_pt-hitting base-coverage and word size may be misleading.
2020-08-19 08:43:08,210 - INFO: Estimated embplant_pt-hitting base-coverage = 140.21
2020-08-19 08:43:08,680 - INFO: Estimated word size(s): 93
2020-08-19 08:43:08,681 - INFO: Setting '-w 93'
2020-08-19 08:43:08,681 - INFO: Setting '--max-extending-len inf'
2020-08-19 08:43:08,875 - INFO: Checking seed reads and parameters finished.

2020-08-19 08:43:08,876 - INFO: Making read index ...
2020-08-19 08:44:36,113 - INFO: 8150988 candidates in all 8228298 reads
2020-08-19 08:44:36,133 - INFO: Pre-grouping reads ...
2020-08-19 08:44:36,133 - INFO: Setting '--pre-w 93'
2020-08-19 08:44:36,814 - INFO: 39166/39166 used/duplicated
2020-08-19 08:44:50,366 - INFO: 636 groups made.
2020-08-19 08:44:51,754 - INFO: Making read index finished.

2020-08-19 08:44:51,755 - INFO: Extending ...
2020-08-19 08:44:51,755 - INFO: Adding initial words ...
2020-08-19 08:44:55,606 - INFO: AW 1768366
2020-08-19 08:45:55,492 - INFO: Round 1: 8150988/8150988 AI 78952 AW 1794490
2020-08-19 08:46:53,491 - INFO: Round 2: 8150988/8150988 AI 78993 AW 1795090
2020-08-19 08:47:52,515 - INFO: Round 3: 8150988/8150988 AI 78993 AW 1795090
2020-08-19 08:47:52,515 - INFO: No more reads found and terminated ...
2020-08-19 08:48:12,527 - INFO: Extending finished.

2020-08-19 08:48:12,761 - INFO: Separating filtered fastq file ...
2020-08-19 08:48:13,918 - INFO: Setting '-k 21,45,65,85,105'
2020-08-19 08:48:13,919 - INFO: Assembling using SPAdes ...
2020-08-19 08:48:13,975 - INFO: spades.py -t 1 -1 Kurobe17_output/filtered_1_paired.fq -2 Kurobe17_output/filtered_2_paired.fq --s1 Kurobe17_output/filtered_1_unpaired.fq --s2 Kurobe17_output/filtered_2_unpaired.fq -k 21,45,65,85,105 -o Kurobe17_output/filtered_spades
2020-08-19 08:49:33,763 - INFO: Insert size = 336.832, deviation = 76.2638, left quantile = 237, right quantile = 432
2020-08-19 08:49:33,764 - INFO: Assembling finished.

2020-08-19 08:49:35,344 - ERROR: Slimming Kurobe17_output/filtered_spades/K105/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K105/slim.log.txt for details.
2020-08-19 08:49:36,660 - ERROR: Slimming Kurobe17_output/filtered_spades/K85/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K85/slim.log.txt for details.
2020-08-19 08:49:38,037 - ERROR: Slimming Kurobe17_output/filtered_spades/K65/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K65/slim.log.txt for details.
2020-08-19 08:49:39,339 - ERROR: Slimming Kurobe17_output/filtered_spades/K45/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K45/slim.log.txt for details.
2020-08-19 08:49:39,341 - ERROR: No valid assembly graph found!

Total cost 677.74 s
Thank you!

Mitochondrial Genome Assembly failed, please help

Hi!
I was trying to assemble the mitochondria of purple maize.

My data is heavy (254,4 GB), with a total of 695510624 paired-end reads in both fastq files.

I run GetOrganelle with the following options:

get_organelle_from_reads.py -1 trimmed_1P.fq -2 trimmed_2P.fq --max-reads=7.5E7 -s zm_mt_ref.fasta --target-genome-size 570000 -o getorg_1 -R 50 -k 21,45,65,85,105 -P 1000000 -F embplant_mt -t 8 --verbose --prefix=zm.mt

Because my dataset was large, I put the option --max-reads=7.5E7. I was afraid of running the program with the whole dataset and make things wrong.

But the mitochondria assembly failed.
The Bandage plot looks like the following:

(this is the one called zm.mtfiltered_K105.assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg in the ouput folder)

Here is my log file:
zm.mtget_org.log.txt

I read the advice you gave to harish0201 (#6) and thought that perhaps I could make something similar?

Please, let me know if there are any parameters I could change to obtain better results. And if perhaps I should use more of my read dataset?

Thanks a lot in advance :)

How to use paired-end library information to confirm an organelle genome configuration with repeats larger than read length/largest k-mer?

Integer end argument expected, got float

Hello
I am testing your tool for assembly both chloroplast and mitochondrion genome
Unfortunately the process stops after spades (see get_org.log)
Any idea on how to solve the issue?
Lorenzo
get_org.log.txt

Extract mitochondrial reads from Oxford nanopore reads

Hi,
I would like to extract plant mitochondrial reads from the whole genome Oxford Nanopore? Do you have any idea which software-related for this? Like GetOrganelle for Illumina reads.
Thank you.

A bug of GetOrganelle 1.6.2a -- fixed

I'm trying to do a mitochondrion assembly for and I get this error when I try to run the assembly. Looks like something Is missing.

get_organelle_from_reads.py -1 ./HA2_USD16090441L_HJM35DSXX_L1_1.fq.gz ./HA2_USD16090441L_HKGF3DSXX_L4_1.fq.gz -2 ./HA2_USD16090441L_HJM35DSXX_L1_2.fq.gz ./HA2_USD16090441L_HKGF3DSXX_L4_2.fq.gz -F embplant_mt -R 50 --memory-save -k 21,45,65,85,105 -s ./mitochondrion.fasta -o mitochondrion

2019-07-12 14:54:02,625 - INFO: Pre-reading fastq ...
2019-07-12 14:54:02,625 - INFO: Estimating reads to use ...
2019-07-12 14:54:03,843 - INFO: Tasting 100000+100000 reads ...
2019-07-12 14:54:16,019 - INFO: Estimating reads to use finished.
2019-07-12 14:54:16,020 - INFO: Unzipping reads file: ./HA2_USD16090441L_HJM35DSXX_L1_1.fq.gz (8906254650 bytes)
2019-07-12 14:54:32,878 - INFO: Unzipping reads file: ./HA2_USD16090441L_HJM35DSXX_L1_2.fq.gz (9090975867 bytes)
2019-07-12 14:54:57,295 - INFO: Counting read qualities ...
2019-07-12 14:54:57,766 - INFO: Identified quality encoding format = Sanger
2019-07-12 14:54:57,768 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2019-07-12 14:54:57,813 - INFO: Mean error rate = 0.0018
2019-07-12 14:54:57,815 - INFO: Counting read lengths ...
2019-07-12 14:55:18,019 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2019-07-12 14:55:18,019 - INFO: Reads used = 3153321+3153321
2019-07-12 14:55:18,019 - INFO: Pre-reading fastq finished.

2019-07-12 14:55:18,019 - INFO: Making seed reads ...
2019-07-12 14:55:18,055 - INFO: Making seed - bowtie2 index ...
2019-07-12 14:55:18,687 - INFO: Making seed - bowtie2 index finished.
2019-07-12 14:55:18,688 - INFO: Mapping reads to seed bowtie2 index ...
2019-07-12 14:57:02,386 - INFO: Mapping finished.
2019-07-12 14:57:02,387 - INFO: Seed reads made: /embplant_mt.initial.fq (129010568 bytes)
2019-07-12 14:57:02,388 - INFO: Making seed reads finished.

2019-07-12 14:57:02,388 - INFO: Checking seed reads and parameters ...
2019-07-12 14:57:02,388 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2019-07-12 14:57:02,388 - INFO: If the result graph is not a circular organelle genome, 
2019-07-12 14:57:02,388 - INFO:   you could adjust the value(s) of '-w'/'-R' for another new run.
2019-07-12 14:57:20,568 - INFO: Pre-assembling mapped reads ...
2019-07-12 14:57:51,703 - INFO: Pre-assembling mapped reads finished.
2019-07-12 14:57:51,704 - INFO: Estimated embplant_mt-hitting base-coverage = 168.78
2019-07-12 14:57:51,704 - INFO: Estimated word size(s): 98
2019-07-12 14:57:51,704 - INFO: Setting '-w 98'
2019-07-12 14:57:51,704 - INFO: Setting '--max-extending-len inf'
2019-07-12 14:57:52,336 - INFO: Checking seed reads and parameters finished.

2019-07-12 14:57:52,336 - INFO: Making read index ...
2019-07-12 14:58:52,684 - INFO: Mem 0.894 G, 6306642 reads
2019-07-12 14:58:53,117 - INFO: Making read index finished.

2019-07-12 14:58:53,117 - INFO: Extending ...
2019-07-12 14:58:53,117 - INFO: Adding initial words ...
2019-07-12 14:59:06,114 - INFO: AW 2048470
2019-07-12 15:00:07,250 - INFO: Round 1: 6306642/6306642 AI 726541 AW 2849312 Mem 0.828
2019-07-12 15:00:50,445 - INFO: Round 2: 6306642/6306642 AI 923061 AW 3246804 Mem 0.892
2019-07-12 15:01:28,567 - INFO: Round 3: 6306642/6306642 AI 947102 AW 3328798 Mem 0.905
2019-07-12 15:02:07,417 - INFO: Round 4: 6306642/6306642 AI 949553 AW 3352248 Mem 0.91
2019-07-12 15:02:45,246 - INFO: Round 5: 6306642/6306642 AI 951483 AW 3370990 Mem 0.915
2019-07-12 15:03:23,420 - INFO: Round 6: 6306642/6306642 AI 953243 AW 3395850 Mem 0.92
2019-07-12 15:04:03,927 - INFO: Round 7: 6306642/6306642 AI 954602 AW 3418200 Mem 0.925
2019-07-12 15:04:42,263 - INFO: Round 8: 6306642/6306642 AI 955506 AW 3433110 Mem 0.931
2019-07-12 15:05:20,903 - INFO: Round 9: 6306642/6306642 AI 956279 AW 3444530 Mem 0.934
2019-07-12 15:05:59,563 - INFO: Round 10: 6306642/6306642 AI 956835 AW 3452146 Mem 0.935
2019-07-12 15:06:38,805 - INFO: Round 11: 6306642/6306642 AI 957266 AW 3457160 Mem 0.936
2019-07-12 15:07:17,549 - INFO: Round 12: 6306642/6306642 AI 957579 AW 3460940 Mem 0.937
2019-07-12 15:07:56,990 - INFO: Round 13: 6306642/6306642 AI 957933 AW 3465170 Mem 0.939
2019-07-12 15:08:39,075 - INFO: Round 14: 6306642/6306642 AI 958284 AW 3468770 Mem 0.94
2019-07-12 15:09:18,349 - INFO: Round 15: 6306642/6306642 AI 958574 AW 3472920 Mem 0.94
2019-07-12 15:09:57,361 - INFO: Round 16: 6306642/6306642 AI 959026 AW 3477170 Mem 0.941
2019-07-12 15:10:35,997 - INFO: Round 17: 6306642/6306642 AI 959426 AW 3481418 Mem 0.941
2019-07-12 15:11:14,720 - INFO: Round 18: 6306642/6306642 AI 959672 AW 3484480 Mem 0.942
2019-07-12 15:11:52,489 - INFO: Round 19: 6306642/6306642 AI 960058 AW 3488320 Mem 0.942
2019-07-12 15:12:30,319 - INFO: Round 20: 6306642/6306642 AI 960393 AW 3491828 Mem 0.943
2019-07-12 15:13:08,071 - INFO: Round 21: 6306642/6306642 AI 960715 AW 3495002 Mem 0.943
2019-07-12 15:13:48,359 - INFO: Round 22: 6306642/6306642 AI 961006 AW 3497694 Mem 0.944
2019-07-12 15:14:27,287 - INFO: Round 23: 6306642/6306642 AI 961224 AW 3499986 Mem 0.944
2019-07-12 15:15:06,349 - INFO: Round 24: 6306642/6306642 AI 961404 AW 3501324 Mem 0.944
2019-07-12 15:15:45,252 - INFO: Round 25: 6306642/6306642 AI 961497 AW 3502046 Mem 0.945
2019-07-12 15:16:24,195 - INFO: Round 26: 6306642/6306642 AI 961521 AW 3502320 Mem 0.945
2019-07-12 15:17:03,111 - INFO: Round 27: 6306642/6306642 AI 961578 AW 3502902 Mem 0.945
2019-07-12 15:17:41,899 - INFO: Round 28: 6306642/6306642 AI 961648 AW 3503366 Mem 0.945
2019-07-12 15:18:20,887 - INFO: Round 29: 6306642/6306642 AI 961699 AW 3503928 Mem 0.945
2019-07-12 15:18:59,841 - INFO: Round 30: 6306642/6306642 AI 961776 AW 3504812 Mem 0.945
2019-07-12 15:19:38,785 - INFO: Round 31: 6306642/6306642 AI 961823 AW 3505080 Mem 0.945
2019-07-12 15:20:17,866 - INFO: Round 32: 6306642/6306642 AI 961876 AW 3505714 Mem 0.945
2019-07-12 15:20:56,856 - INFO: Round 33: 6306642/6306642 AI 961924 AW 3506328 Mem 0.945
2019-07-12 15:21:35,929 - INFO: Round 34: 6306642/6306642 AI 961974 AW 3506702 Mem 0.945
2019-07-12 15:22:15,072 - INFO: Round 35: 6306642/6306642 AI 961996 AW 3506968 Mem 0.945
2019-07-12 15:22:54,365 - INFO: Round 36: 6306642/6306642 AI 962045 AW 3507534 Mem 0.945
2019-07-12 15:23:33,643 - INFO: Round 37: 6306642/6306642 AI 962170 AW 3508680 Mem 0.946
2019-07-12 15:24:12,745 - INFO: Round 38: 6306642/6306642 AI 962249 AW 3509478 Mem 0.946
2019-07-12 15:24:50,125 - INFO: Round 39: 6306642/6306642 AI 962296 AW 3509930 Mem 0.946
2019-07-12 15:25:27,673 - INFO: Round 40: 6306642/6306642 AI 962349 AW 3510238 Mem 0.946
2019-07-12 15:26:05,631 - INFO: Round 41: 6306642/6306642 AI 962352 AW 3510256 Mem 0.946
2019-07-12 15:26:44,565 - INFO: Round 42: 6306642/6306642 AI 962352 AW 3510256 Mem 0.946
2019-07-12 15:26:44,565 - INFO: No more reads found and terminated ...
2019-07-12 15:27:03,253 - INFO: Extending finished.

2019-07-12 15:27:03,643 - INFO: Separating filtered fastq file ... 
2019-07-12 15:27:11,428 - INFO: Setting '-k 21,45,65,85,105'
2019-07-12 15:27:11,428 - INFO: Assembling using SPAdes ...
2019-07-12 15:37:22,731 - INFO: Insert size = 254.621, deviation = 59.3392, left quantile = 186, right quantile = 332
2019-07-12 15:37:22,732 - INFO: Assembling finished.

2019-07-12 15:37:22,732 - INFO: Slimming assembly graphs ...
2019-07-12 15:37:31,381 - INFO: Slimming _mitochondrion/filtered_spades/K105/assembly_graph.fastg finished!
2019-07-12 15:37:34,088 - INFO: Slimming _mitochondrion/filtered_spades/K85/assembly_graph.fastg finished!
2019-07-12 15:37:36,850 - INFO: Slimming _mitochondrion/filtered_spades/K65/assembly_graph.fastg finished!
2019-07-12 15:37:39,071 - INFO: Slimming _mitochondrion/filtered_spades/K45/assembly_graph.fastg finished!
2019-07-12 15:37:39,072 - INFO: Slimming assembly graphs finished

2019-07-12 15:37:39,084 - INFO: Extracting embplant_mt from the assemblies ...
2019-07-12 15:37:39,087 - INFO: Disentangling _mitochondrion/filtered_spades/K105/assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg as a circular genome ... 
2019-07-12 15:37:39,151 - ERROR: 
Traceback (most recent call last):
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3346, in extract_organelle_genome
    temp_graph=graph_temp_file)
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3307, in disentangle_assembly
    acyclic_allowed_in=here_acyclic_allowed, verbose_in=here_verbose, in_temp_graph=temp_graph)
  File "/home/[email protected]/Hagop/GetOrganelle/GetOrganelleLib/pipe_control_func.py", line 85, in func_modified
    r = func(*args, **kwargs)
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3193, in disentangle_inside
    temp_graph=in_temp_graph)
  File "/home/[email protected]/Hagop/GetOrganelle/GetOrganelleLib/assembly_parser.py", line 1941, in find_target_graph
    str(new_assembly.vertex_info[del_v].other_attr["tags"][database_name]))
KeyError: 'tags'
2019-07-12 15:37:39,171 - ERROR: 
Traceback (most recent call last):
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3346, in extract_organelle_genome
    temp_graph=graph_temp_file)
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3307, in disentangle_assembly
    acyclic_allowed_in=here_acyclic_allowed, verbose_in=here_verbose, in_temp_graph=temp_graph)
  File "/home/[email protected]/Hagop/GetOrganelle/GetOrganelleLib/pipe_control_func.py", line 85, in func_modified
    r = func(*args, **kwargs)
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3193, in disentangle_inside
    temp_graph=in_temp_graph)
  File "/home/[email protected]/Hagop/GetOrganelle/GetOrganelleLib/assembly_parser.py", line 1941, in find_target_graph
    str(new_assembly.vertex_info[del_v].other_attr["tags"][database_name]))
KeyError: 'tags'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3815, in main
    options=options)
  File "/home/[email protected]/Hagop/./GetOrganelle/get_organelle_from_reads.py", line 3359, in extract_organelle_genome
    sys.exit()
SystemExit

Total cost 2617.58 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!

Assembling failed

I try to assemble chloroplast from raw reads using
get_organelle_reads.py -1 /sanhome2/trimmed/out2045_1.clean.fastq -2 /sanhome2/trimmed/out2045_2.clean.fastq -s pc_ref.fa -w 103 -J 3 -M 5 -o chloro_out -R 5 -k 75,85,95,105 -P 1000000
I have about 70 000 000 150 PE reads.

I got error assembling failed and I thinkj because filtred paired reads files were empty and I don't know why.
Below somes logfiles to undersatnd this issue:

2018-07-20 17:50:45,343 - INFO: Separating filtered fastq file finished!
2018-07-20 17:50:47,679 - INFO: Assembling using SPAdes ...
2018-07-20 17:50:48,293 - ERROR: Error in SPAdes:
== Error == system call for: "['/home1/software/SPAdes-3.11.1-linux/bin/hammer', '/sanhome2/Organnelle/chloro_out/filtered_spades/corrected/configs/config.info']" finished abnormally, err code: 255

2018-07-20 17:50:48,298 - ERROR: Assembling failed.

Total Calc-cost 20067.3784549
Thanks you!
#############
config.info
; = HAMMER =
; input options: working dir, input files, offset, and possibly kmers
dataset /sanhome2/Organnelle/chloro_out/filtered_spades/input_dataset.yaml
input_working_dir /sanhome2/Organnelle/chloro_out/filtered_spades/tmp/hammer_BH7RTS
input_trim_quality 4
input_qvoffset
output_dir /sanhome2/Organnelle/chloro_out/filtered_spades/corrected

; == HAMMER GENERAL ==
; general options
general_do_everything_after_first_iteration 1
general_hard_memory_limit 250
general_max_nthreads 4
general_tau 1
general_max_iterations 1
general_debug 0

; count k-mers
count_do 1
count_numfiles 16
count_merge_nthreads 4
count_split_buffer 0
count_filter_singletons 0

; hamming graph clustering
hamming_do 1
hamming_blocksize_quadratic_threshold 50

; bayesian subclustering
bayes_do 1
bayes_nthreads 4
bayes_singleton_threshold 0.995
bayes_nonsingleton_threshold 0.9
bayes_use_hamming_dist 0
bayes_discard_only_singletons 0
bayes_debug_output 0
bayes_hammer_mode 0
bayes_write_solid_kmers 0
bayes_write_bad_kmers 0
bayes_initial_refine 1

; iterative expansion step
expand_do 1
expand_max_iterations 25
expand_nthreads 4
expand_write_each_iteration 0
expand_write_kmers_result 0

; read correction
correct_do 1
correct_discard_bad 0
correct_use_threshold 1
correct_threshold 0.98
correct_nthreads 4
correct_readbuffer 100000
correct_stats 1

Thank you for youre help!

kinggerm / getorganelle Goto Github PK

getorganelle's Issues

Total cost 347.66 s Please email [email protected] or [email protected] if you find bugs! Please provide me with the get_org.log.txt file!

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Total cost 347.66 s
Please email [email protected] or [email protected] if you find bugs!
Please provide me with the get_org.log.txt file!