Comments (11)
Apologize for the late reply.
Could you add --verbose to you command? Have you got a slim.log.txt file in the output directory?
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Did this ever get resolved? I am having a similar issue. It does not say that slimming failed so I'm having problems troubleshooting, but it doesn't seem to be saving the slimmed assembly graph so the next step can't find it (I think?).
the slimmed_assembly_graph.slim.log.txt log only contains
2023-12-14 21:39:00,397 - INFO: Slimming file 1/1: /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50/initial_assembly_graph.gfa
and the get_org.log.txt contains
GetOrganelle v1.7.7.0
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 3.9.18 (main, Sep 11 2023, 13:41:44) [GCC 11.2.0]
PLATFORM: Linux wbn069 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.7.0; numpy 1.26.2; sympy 1.12; scipy 1.11.4
DEPENDENCIES: Blast 2.12.0; Bandage 0.8.1
GETORG_PATH=/home/footeim/.GetOrganelle
LABEL DB: animal_mt 0.0.1
WORKING DIR: /scale_wlg_nobackup/filesets/nobackup/vuw03922/scripts/Chapter3/extract_mitogenome
/nesi/project/vuw03922/bandage/bin/get_organelle_from_assembly.py -F animal_mt -g /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/assemblies/flye/1_raw/blue-45G_q8_h50/assembly_graph.gfa -o /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50 -t 10 --overwrite --verbose
2023-12-14 21:38:54,334 - INFO: Processing assembly graph ...
2023-12-14 21:38:57,246 - INFO: Processing assembly graph finished.
2023-12-14 21:38:57,247 - INFO: Slimming assembly graph ...
2023-12-14 21:38:57,251 - INFO: /scale_wlg_persistent/filesets/project/vuw03922/bandage/bin/slim_graph.py -t 10 /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50/initial_assembly_graph.gfa --out-base /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50/slimmed_assembly_graph --include-priority /home/footeim/.GetOrganelle/LabelDatabase/animal_mt.fasta --log --wrapper --verbose --max-slim-extending-len 12500
2023-12-14 21:39:02,390 - INFO: 2023-12-14 21:39:00,397 - INFO: Slimming file 1/1: /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50/initial_assembly_graph.gfa
2023-12-14 21:39:02,390 - INFO: Slimming /nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50/initial_assembly_graph.gfa finished!
2023-12-14 21:39:02,390 - ERROR:
Traceback (most recent call last):
File "/nesi/project/vuw03922/bandage/bin/get_organelle_from_assembly.py", line 1021, in main
if os.path.getsize(slimmed_graph_file) == 0:
File "/nesi/project/vuw03922/bandage/lib/python3.9/genericpath.py", line 50, in getsize
return os.stat(filename).st_size
FileNotFoundError: [Errno 2] No such file or directory: '/nesi/nobackup/vuw03922/projects/AntipodeanAlbatross/data/Chapter3/mitogenome/blue-45G_q8_h50/slimmed_assembly_graph.gfa'
Total cost 26.27 s
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Thanks for reaching out!
To better help you, could you add --verbose to your command? Have you got a slim.log.txt file in the output directory?
from getorganelle.
Thanks @JianjunJin. Sorry I forgot to mention I tried it with --verbose in the command as per the previous suggestion and the above output is what that gave me. There is no slim.log.txt file in the output directory, only the get_org.log.txt and slimmed_assembly_graph.slim.log.txt that I included above.
from getorganelle.
Would also appreciate this being solved. Having the exact same issue.
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Hi all, I cannot reproduce it from my side. But I would like to help.
Could you please test if slim_graph.py -h
and blastn -h
will be running correctly in your environment?
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from getorganelle.
@alistairhockey Glad that you solved it! And thanks for letting me know.
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Hi @alistairhockey, thanks for the info. Would you mind giving me a little more specific detail on how you solved this? I'm relatively new to all this, so can't quite follow your directions above. I have the py scripts in my_env/bin/, but I'm not sure where else you meant you had them that you removed them from?
Thank you!! Much appreciated
from getorganelle.
Hi @imogen-foote, I'd sugest the following:
- Uninstall GetOrganelle and all .py scripts associated (e.g. get_organelle_from_reads.py).
- Create a conda environment with GetOrganelle installed (conda create env name -c bioconda GetOrganelle)
- Activate the conda environment.
- Test it out!
I found that having old GetOrganelle .py scripts in my /bin directory was causing the issue. Best to clean everything up and have the program running in a self-contained environment.
Cheers.
from getorganelle.
Thanks so much @alistairhockey. I think I was initially a bit confused because I didn't have GetOrganelles installed anywhere else, other than my conda environment. Anyway I also found a solution, which was to remove the conda environment and create it fresh, using mamba create (I got a bunch of dependency issues using conda but mamba seems to solve them) and installing both bandage and GetOrganelles at the time of creation (previously I created it with bandage and installed getorganelles after).
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Related Issues (20)
- Invalid information provided HOT 1
- dogged request of help with Invalid version spec: =2.7 HOT 5
- ERROR: slimming the pre-assembled graph failed HOT 1
- not able to to run "summary_get_organelle_output.py" and "IndexError:list out of range" HOT 1
- I have problem with running getorganelle in cluster HOT 1
- Crashes while running GetOrganelle when I try to use all raw reads HOT 2
- Slimming failed and no valid assembly graph found HOT 6
- How to jugde circular? HOT 1
- How to provide multiple sets of paired-reads? HOT 1
- Incomplete animal mitochondria HOT 11
- “Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?” AND the assemble length range different from reference HOT 2
- Please fix SPAdes citation HOT 2
- Estimated XX base-coverage = 0.00 HOT 5
- Disentangling failed: 'Unrecognized GFA version number: 1.2' HOT 2
- BLAST Database error: Error: Not a valid version 4 database. HOT 3
- ERROR ON UNZIPPING THE .gz file HOT 3
- ERROR: Disentangling failed: Failed in 'from scipy import stats, inf, log'! HOT 3
- Regarding the Use of Incomplete Plant Mitochondrial Genome Assembly Outputs for Subsequent Analysis HOT 2
- failing from flye assembly graph of a phage genome with 4 circular paths HOT 5
- Disentangling failed: 'Unable to generate result with single copy vertex percentage < 50%' HOT 20
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