Problem with clusterseq

[mrozwandowicz]

Hi,

I am very excited about using mgefinder, but so far I cannot make it work. I successfully run the script with a test dataset. However, multiple trials with different isolates and different reference genomes gave me the same error.

Error in job clusterseq while creating output file workdir/03.results/R27/01.clusterseq.R27.tsv. RuleException: CalledProcessError in line 259 of /home/rozwandm/.conda/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile: Command 'mgefinder clusterseq -minsize 70 -maxsize 200000 --threads 1 --memory 16000 workdir/01.mgefinder/R27/R27.all_inferseq_database.txt -o workdir/03.results/R27/01.clusterseq.R27.tsv' returned non-zero exit status 1. File "/home/rozwandm/.conda/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile", line 259, in __rule_clusterseq File "/home/rozwandm/.conda/envs/mgefinder/lib/python3.6/concurrent/futures/thread.py", line 56, in run Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message

Thank you in advance for your help, Marta

[durrantmm]

Hello!

Thanks for asking this.

What error do you get when you run:

mgefinder clusterseq -minsize 70 -maxsize 200000 --threads 1 --memory 16000 workdir/01.mgefinder/R27/R27.all_inferseq_database.txt -o workdir/03.results/R27/01.clusterseq.R27.tsv

when the mgefinder conda environment is activated?

[mrozwandowicz]

I got this error message:

IndexError: list index out of range

[durrantmm]

This is a strange one, how many samples are you analyzing?

[mrozwandowicz]

I always tried one sample at the time. Because I had problems and I thought the reference genome might be the problem, I tried multiple references, but always one at the time.

[durrantmm]

Great, could you please send me one of the samples that failed so I can test it? Thanks.

[mrozwandowicz]

I send you all of the files on this email address: mdurrant@stanford.edu

[durrantmm]

Thanks for sending over your files.

I was able to recreate the error you found. The issue was with how you named the files in your working directory. Please refer to the tutorial to see exactly how to set up your working directory.

You had it set up like this:

workdir/
├── 00.assembly/
│   └── 15S04545-4.fasta.fna
├── 00.bam/
│   ├── 15S04545-4.bam
│   └── 15S04545-4.bam.bai
└── 00.genome/
    └── R27.fna

I fixed it so that it looked like this:

workdir/
├── 00.assembly/
│   └── 15S04545-4.fna
├── 00.bam/
│   ├── 15S04545-4.R27.bam
│   └── 15S04545-4.R27.bam.bai
└── 00.genome/
    └── R27.fna

And that fixed it.

I hope that helps! Make sure you include all of your isolates in a single working directory.