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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
105 stars 16 forks source link

KeyError #27

Closed Kylies5 closed 3 years ago

Kylies5 commented 3 years ago

Hello, do you know what is causing this error and how to fix it?

KeyError: 'emb|FRDD01000003.1|' Error in job pair while creating output file /scratch/aubksw/MGEfinder/MGEfinder/cluster4/01.mgefinder/XretroflexusSp953/Xsp60/02.pair.Xsp60.XretroflexusSp953.tsv. RuleException: CalledProcessError in line 109 of /home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile: Command ' mgefinder pair -maxdr 20 -minq 20 -minial 21 -maxjsp 0.15 -lins 30 /scratch/aubksw/MGEfinder/MGEfinder/cluster4/01.mgefinder/XretroflexusSp953/Xsp60/01.find.Xsp60.XretroflexusSp953.tsv $ ' returned non-zero exit status 1.

durrantmm commented 3 years ago

Thanks for sharing this. Could you please send me the input files for this particular analysis? Not all of them, just the sample Xsp60.XretroflexusSp953

Kylies5 commented 3 years ago

How do I send the files?

durrantmm commented 3 years ago

However you like, you can zip them up and attach them in your next response to this thread, for example.

Kylies5 commented 3 years ago

Hello, here are the files: 00.genome - XretroflexusSp953.fna.zip 00.assembly - Xsp60.fna.zip

Kylies5 commented 3 years ago

00.bam- Xsp60.XretroflexusSp953.bam.bai.zip

Kylies5 commented 3 years ago

The other bam file will not upload

durrantmm commented 3 years ago

Ok, well I will need the BAM file. Could you upload it to google drive or dropbox and share a link?

Kylies5 commented 3 years ago

https://drive.google.com/drive/folders/1vAACS7RxB_o1ap_Fy9dzVlGCP5QNOC3-?usp=sharing