Comments (15)
Hey LinXing,
Yeah, that seems to have fixed the issue! Both sample now run to completion 😄
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No problem and thank you for the rapid fix!
from cobra.
Hi,
Thank you for your interest in COBRA, I am glad it helps for your analyses.
Regarding these two samples, could you please share these files with me , (1) COBRA_end_joining_pairs.txt (2) COBRA_potential_joining_paths.txt and (3) debug file?
Thank you.
Best,
LINXING
from cobra.
Sure, here are those 3 files for sample 1 (key error in this case was 'NODE_67_length_39995_cov_222.169830')
COBRA_end_joining_pairs.txt
COBRA_potential_joining_paths.txt
debug.txt
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And here they are for sample 2 (key error here was 'NODE_404_length_6556_cov_28.183972')
COBRA_end_joining_pairs.txt
COBRA_potential_joining_paths.txt
debug.txt
from cobra.
Thank you Chris. I will take a look ASAP and let you know what is the wrong.
from cobra.
And here they are for sample 2 (key error here was 'NODE_404_length_6556_cov_28.183972')
COBRA_end_joining_pairs.txt COBRA_potential_joining_paths.txt debug.txt
Hi Chirs, unfortunately I was not able to locate the bug with the files you provided. Do you mind sharing all the input files of this sample, so I can run COBRA on my end and try to debug it? No worries if you do not want to do so.
LINXING
from cobra.
Yeah sure no problem, I'll send them onto the gmail address you provided in a different issue post. Thanks again for taking a look at the issue!
In case you need it here is the command i'm running for sample 1 (so same for sample 2 except paths to files)
cobra-meta -f data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds.fasta -q data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds_over_2.5kb.fasta -
c data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds.coverage.formatted.txt -m data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds_sorted.bam -a metaspa
des -mink 21 -maxk 55 -t 10 -o data/processed/assemblies/spades_CTRLM08LongB03Faeces/cobra/
from cobra.
Sent :)
from cobra.
Sent :)
Hi Chris, unfortunately I do not see the email. Could you please confirm?
from cobra.
I sent it to the linkingchanATgmailDOTcom address you posted in another issue. Is this not the correct email?
from cobra.
i sent it via wetransfer so may be in your spam if that is the correct email
from cobra.
I have checked and did not see it anywhere. My email address is [email protected]. Could you please share using googledoc or dropbox?
from cobra.
Hi Chris, I think I was able to fix the bug. Could you please try this version and let me know if it works for you or not? Thank you.
cobra_test.py.zip
from cobra.
That's good to know. Thank you for help. I will release a new version asap.
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Related Issues (20)
- biopython issue / GC deprecation HOT 7
- Randomly not getting full output HOT 6
- Application of COBRA to stool whole metagenome datasets HOT 2
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- The role of cobra in classic virome pipeline HOT 4
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- Tiny dataset is available ?
- Feasibility of COBRA for Metatranscriptomic Data HOT 3
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- new installation of miniconda I run into this error HOT 7
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