error at intervals step

[shaul-pollak]

First off - thanks for this tool!
i ran the workflow on the test dataset with no problems, but I've been trying to test it on some genomes we sequenced, and am getting an error at the interval finding step.

This is the error message:

Error executing process > 'uv:intervals (1)'

Caused by:
  Process `uv:intervals (1)` terminated with an error exit status (1)

Command executed:

  find_phage_breakpoints.py --genome renamed_contigs.fasta --frames reading_frames.faa --hits aln.m8 --threshold 1 --names contig_names.txt --outdir results
  cat results/*.bed > tmp
  bedtools sort -i tmp > putative.bed

Command exit status:
  1

Command output:
  (empty)

Command error:
  cat: 'results/*.bed': No such file or directory

Looking at the aln.m8 file in the relevant dir shows only a single hit.

[phiweger]

hm. likely I'm not catching the case when there are no results in this step -- could you send me the corresponding genome to replicate?

[shaul-pollak]

Thanks for the quick reply!
here it is.
genome.txt

[limeng849]

do there any solutions about this issue?

[phiweger]

what error msg do you get? what genome are you using as input?

[phiweger]

Ok this error occurs when there are no prophages found in the genome. Will catch this error in the next release, thx for reporting.