Hello! I’m new here and I have been redirected from GitHub, I hope the format I used there is ok.
Running Humann 3.6 (from a Galaxy Singularity image) using as database
mpa_vJan21_CHOCOPhlAnSGB_202103, the program exited with error.
humann \ -i “2MO24h.fq.gz” -o “out” \ –nucleotide-database $DB/chocophlan \ –protein-database $DB/uniref \ –metaphlan-options=" --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $DB/mpa " \ –threads 24
I paste the log from the last successful messages to the traceback:
Total gene families after translated alignment: 233101 Unaligned reads after translated alignment: 24.0780298738 % Computing gene families ... Computing pathways abundance and coverage ... Command error: Traceback (most recent call last): File "/usr/local/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py", line 934, in <module> Orth2Path(infile = anyfile, mpsfile = mpsfile, reportfile = reportfile, detailfile = detailfile, whichdb = "ANY", mapfile=mapfile) File "/usr/local/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py", line 901, in Orth2Path map = test.Orth2PathMin(famidxlist=, famnamelist=orthlist, famcount=orthcount, mpsfile=mpsfile) File "/usr/local/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py", line 576, in Orth2PathMin self.GetLPOut(lpout) File "/usr/local/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py", line 671, in GetLPOut if len(keeppath) != MINimum: UnboundLocalError: local variable 'MINimum' referenced before assignment CRITICAL ERROR: Unable to process all thread commands. Error message returned from command for thread task 42: /usr/local/bin/python3.10 /usr/local/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py -any out/2MO24h_humann_temp/tmplsqts9nu/tmpsijjmk4n -map out/2MO24h_humann_temp/tmplsqts9nu/tmpebjakbhe -report out/2MO24h_humann_temp/tmplsqts9nu/tmpd5zbfro7 -details out/2MO24h_humann_temp/tmplsqts9nu/tmpditlrqyy -mps out/2MO24h_humann_temp/tmplsqts9nu/tmp27b6n9ua
In the output directory there are these files:
- 2MO24h_humann_temp/ (contains the whole 2MO24h_metaphlan_bugs_list.tsv)
The line triggering the error seems to be neede while parsing a file (in my case
2MO24h_humann_temp/tmplsqts9nu/tmp27b6n9ua.LPout), which starts with:
Problem: PATH Rows: 73 Columns: 209 (209 integer, 209 binary) Non-zeros: 362 Status: INTEGER OPTIMAL Objective: NUM = 38 (MINimum)
and the line with “Objective” has no tabs in it.
Do you have any guidance? With some samples this command worked, with others got this error.
Thanks a million!