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Missing COBRA_retrieved_for_joining
contig file
#30
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Hi, Sorry to hear that you have problem running COBRA. We noticed this issue and have been working on it. Could you please let me know (1) did you re-run on the same sample? (2) every time the Thank you. Best, |
Hi @linxingchen, Thanks for the quick reply! (1) I removed the Cobra output folder and re-ran on the same sample. Thanks! |
hi @Vini2 thanks for the information. If possible please share me the "potential_join_path" file so I can have a look if these three are in the same path. We have been working on this but please give us more time to fix it. Thank you. |
Hi @linxingchen, Here is the file you requested. Let me know if you need further details. Thanks for taking a look at this issue. |
Thank you. These three contigs are not in the same path, I have no idea why the file does not existed. I am wondering if you could run another sample and see if it will happen again. |
Hi @linxingchen, I did a bit of debugging and I think some edge cases cause the errors. This time I got that In line 1747 when calling
Then it tries to count sequences from Here I came across some more edge cases which I couldn't test out in detail. How would you recommend running these contigs? I'm not sure how to check if a contig is a subset or not. Would running them one by one be better? Appreciate any suggestions. I'll try running on another sample as well. Thanks! |
Hi @Vini2, Thanks for taking a deep look at the issue. Sorry for my delayed reply. Did you still run the previous same sample? You will avoid the error if you run them one by one. However, at the end of day, I have to fix this issue, hopefully in the next week (stuck by grant proposal for now). Best, |
Hi @Vini2, Sorry for my delayed reply on this, @Hocnonsense re-wrote most parts of the script, it will be great if you could try it (enclosed) and see if your issue has been resolved or not. Thank you. |
Hello Cobra authors!
Thanks for building this tool.
I keep getting this error of a contig file not being created.
Every time I try re-running, it fails at this stage with a
FileNotFoundError
for a different contig.This is my Cobra command. I'm using the latest version (version 1.2.3).
My
query_contigs.fasta
file contains about 2300 contig sequences. I've also attached the log file of the run.log.txt
Any advice on how to fix this error and get Cobra running will be appreciated.
Thanks!
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