Apologies for lack of clarity
re: itsxpress
if I demultiplex single-end sequences in qiime (qiime demux emp-single), and then run itsxpress (qiime itsxpress trim-single) I get the following error:
Plugin error from itsxpress:
Command ‘[‘vsearch’, ‘–cluster_size’, ‘/tmp/itsxpress_fp0p5hbq/seq.fq.gz’, ‘–centroids’, ‘/tmp/itsxpress_fp0p5hbq/rep.fa’, ‘–uc’, ‘/tmp/itsxpress_fp0p5hbq/uc.txt’, ‘–strand’, ‘both’, ‘–id’, ‘0.995’, ‘–threads’, ‘1’]’ returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-oopcu8c_.log
Looking in the log file, the error arises from vsearch
vsearch v2.7.0_linux_x86_64, 251.8GB RAM, 32 cores
Fatal error: File too small
subprocess.CalledProcessError: Command ‘[‘vsearch’, ‘–cluster_size’, ‘/tmp/itsxpress_fp0p5hbq/seq.fq.gz’, ‘–centroids’, ‘/tmp/itsxpress_fp0p5hbq/rep.fa’, ‘–uc’, ‘/tmp/itsxpress_fp0p5hbq/uc.txt’, ‘–strand’, ‘both’, ‘–id’, ‘0.995’, ‘–threads’, ‘1’]’ returned non-zero exit status 1.
Checking the dir w/ tmp filles:
ls -l /tmp/itsxpress_fp0p5hbq/
total 6872
-rw-r–r-- 1 qiime2 qiime2 0 Mar 19 16:18 rep.fa
-rw-r–r-- 1 qiime2 qiime2 20 Mar 19 16:18 seq.fq.gz
-rw-r–r-- 1 qiime2 qiime2 3524967 Mar 19 16:18 seq_r1.fq.gz
-rw-r–r-- 1 qiime2 qiime2 3502500 Mar 19 16:18 seq_r2.fq.gz
-rw-r–r-- 1 qiime2 qiime2 0 Mar 19 16:18 uc.txt
I’m not sure why htere is a .r2 seq file for silngle-end method, is this the basis for the vsearch error?
Hope htat helps
Charles