Hello,
I am trying to use ITSxpress to trim primers and remove conserved regions as it describes.
I used the following script with a SLURM submission to the HPCC at my university.
This is being run on the output of a MiSeq run 2x 300bp V3 chemistry that was demultiplexed by our sequencing core that I imported to qiime2 with a manifest.
cd /mnt/home/USERNAME/timecourse/
conda activate qiime2-2022.8
qiime itsxpress trim-pair-output-unmerged
--i-per-sample-sequences paired-end-demux.qza
--p-region ALL
--p-taxa F
--p-threads 2
--o-trimmed trimmedITSxpress.qza
Running this, I get the following error:
Plugin error from itsxpress:
Command '['hmmsearch', '--domtblout', '/tmp/local/99083/itsxpress_rlwix5pn/domtbl.txt', '-T', '10', '--cpu', '2', '--tformat', 'fasta', '--F1', '1e-6', '--F2', '1e-6', '--F3', '1e-6', '/mnt/home/USERNAME/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/itsxpress/ITSx_db/HMMs/F.hmm', '/tmp/local/99083/itsxpress_rlwix5pn/rep.fa']' returned non-zero exit status 1.
Debug info has been saved to /tmp/local/99083/qiime2-q2cli-err-gzzxnfh7.log
Searching other issues people have encountered similar to this I saw mention of validating the metadata with Keemei. My metadata was valid, so I do not believe it is that.
Unfortunately, with how our HPCC operates, the debug info is being saved to a location that is deleted immediately upon the completion of the SLURM job.
From looking into things, "returned non-zero exit status 1" broadly indicates a failure in the code's execution, sometimes regarding finding files/inputs. The file ".../ITSx_db/HMMs/F.hmm" does exist in the proper location, but I cannot verify anything regarding the /tmp/ files on account of them being deleted upon job completion to my knowledge.
Unfortunately I haven't really been able to find a great answer for this by searching the forums, and the information that would help me seems to be difficult to access on account of how our HPCC operates.
EDIT: I used --verbose to get a bit more info. The holdup seems to happen with:
Error: Sequence file /tmp/local/102975/itsxpress_mb8uae5p/rep.fa is empty or misformatted
Does anyone have insights into what could be causing this with ITSxpress specifically, or this class of error in general?
Forum!