Comments (3)
Hi Alex,
I recommend you to run the stable releases 1.1
https://github.com/marbl/MetaCompass/releases/tag/1.1
The new release will be available next the week.
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Thanks you for your prompt reply! I downloaded and installed the stable version. Running
python go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -P tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -o example1_output -m 1 -t 4
the output is
confirming file containing reference genomes exists..
[OK]
checking for dependencies (Bowtie2, Blast, kmermask, Snakemake, etc)
Bowtie2--->[OK]
/home/talex/.pyenv/versions/miniconda3-latest/bin/blastn
Blast+--->[OK]
/home/talex/apps/MetaCompass-1.1/bin/kmer-mask
kmer-mask--->[OK]
/home/talex/.pyenv/versions/miniconda3-latest/bin/snakemake
Snakemake--->[OK]
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 assemble_unmapped
1 bam_sort
1 bowtie2_map
1 build_contigs
1 create_tsv
1 join_contigs
1 merge_reads
1 pilon_contigs
1 pilon_map
1 sam_to_bam
11
Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807} [53/14267]
Ready jobs (1):
merge_reads
Selected jobs (1):
merge_reads
Resources after job selection: {'_cores': 3, '_nodes': 9223372036854775806}
---merge fastq reads
Releasing 1 _cores (now 4).
Releasing 1 _nodes (now 9223372036854775807).
1 of 11 steps (9%) done
Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807}
Ready jobs (1):
bowtie2_map
Selected jobs (1):
bowtie2_map
Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}
---Build index .
Full Traceback (most recent call last):
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 784, in run_wrapper
version)
File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 86, in __rule_bowtie2_map
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/shell.py", line 74, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.a
ssembly.out/thao2000.index 1>> example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_outp
ut/thao2000.0.assembly.out/thao2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_outp
ut/thao2000.0.bowtie2map.log 2>&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_outpu
t/thao2000.0.assembly.out/thao2000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1
Error in job bowtie2_map while creating output files example1_output/thao2000.0.assembly.out/thao2000.index, example1_output/thao2000.0.assembly.out/thao2000.
index, example1_output/thao2000.0.assembly.out/thao2000.sam.
Full Traceback (most recent call last):
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 784, in run_wrapper
version)
File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 86, in __rule_bowtie2_map
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/shell.py", line 74, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.a
ssembly.out/thao2000.index 1>> example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_outp
ut/thao2000.0.assembly.out/thao2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_outp
ut/thao2000.0.bowtie2map.log 2>&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_outpu
t/thao2000.0.assembly.out/thao2000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 247, in _callback
raise ex
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/concurrent/futures/thread.py", line 55, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 798, in run_wrapper
show_traceback=True))
snakemake.exceptions.RuleException: CalledProcessError in line 50 of /home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py:
Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.assembly.out/thao2000.index 1>>
example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_output/thao2000.0.assembly.out/thao
2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_output/thao2000.0.bowtie2map.log 2>
&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_output/thao2000.0.assembly.out/thao2
000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1
File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 50, in __rule_bowtie2_map
RuleException:
CalledProcessError in line 50 of /home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py:
Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.assembly.out/thao2000.index 1>>
example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_output/thao2000.0.assembly.out/thao
2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_output/thao2000.0.bowtie2map.log 2>
&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_output/thao2000.0.assembly.out/thao2
000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1
File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 50, in __rule_bowtie2_map
File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Removing output files of failed job bowtie2_map since they might be corrupted:
example1_output/thao2000.0.assembly.out/thao2000.index, example1_output/thao2000.0.assembly.out/thao2000.index
Releasing 4 _cores (now 4).
Releasing 1 _nodes (now 9223372036854775807).
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
unlocking
removing lock
removing lock
removed all locks
ERROR: snakemake command failed; exiting..
the example_output dir contains
Candidatus_Carsonella_ruddii_HT_Thao2000.fasta thao2000.0.assembly.out thao2000.fasta thao2000.marker.match.1.fastq thao2000.merged.fq
I suppose I should wait until next week or so?
from metacompass.
I'm trying to run the tutorial example with the new release (https://github.com/marbl/MetaCompass/releases/tag/paper-v1.0). After checking dependencies and installing I ran
python go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -P tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -o example1_output -m 1 -t 4
. I am no longer getting these errors, instead I am getting Issue #7. I'll mark this as closed
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Related Issues (20)
- Error in executors.py -- megahit HOT 1
- enable --nolock in snakemake workflow, or --unlock on command line HOT 4
- Specifying multiple .fasta reference genomes? HOT 4
- Error with kmer-mask if input is gz compressed HOT 2
- Snakemake error while running MetaCompass (unrecognized arguments: -T) HOT 5
- Using MetaCompass with GTDB instead of refseq HOT 4
- Error when running MetaCompass HOT 4
- one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode HOT 19
- Intallation problems (MacOS Catalina)
- Bowtie2 error
- snakemake: error: unrecognized arguments: -T HOT 5
- Error in job reference_selection HOT 2
- Refseq-free installation? HOT 1
- Error --pilon polish contigs HOT 1
- Could not open reference sequences file /refseq/markers/genome2markers.length HOT 1
- Error when running MetaCompass HOT 1
- snakemake: error: argument **-T/--restart-times: expected one argument** HOT 3
- TypeError in line 133 of metacompass.iter0.ref.py, returned non-zero exit status 1 if TypeError resolved
- Errors from reference-guided mode, using example data HOT 4
- Error in job reference_recruitment while creating output files HOT 6
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