Hi Dears,
I used VFDB & CARD with UniRef90 (ref) to make the markers, then used the sra file (ERR1018195, with kneaddata processed, the input files were paired-end files) to shortbred with VF_shortbred.fasta,and the reported the error with:
Working on file 1 of 1
usearch v11.0.667_i86linux32, 4.0Gb RAM (528Gb total), 80 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch
00:02 31Mb 100.0% Rows
00:02 31Mb Reading pointers...done.
00:02 31Mb Reading db seqs...done.
00:02 65Mb 0.1% Searching fasta.fna, 0.0% matched
usearch --usearch_local $path/tmp/fasta.fna --db $path/card.fasta.udb --id 80.0 --userout $pathtmp/wgs_01out_01.out --userfields query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits+ql+tl+qs+ts --maxaccepts 1 --maxrejects 32 --threads 40
---Fatal error---
../wordparams.cpp(171) assert failed: MinFractId >= 0.0 && MinFractId <= 1.0
Traceback (most recent call last):
File "$path/miniconda3/envs/shortbred/bin/shortbred_quantify.py", line 543, in <module>
iThreads=args.iThreads,dID=args.dID, iAccepts=args.iMaxHits, iRejects=args.iMaxRejects,strUSEARCH=args.strUSEARCH )
File "$path/miniconda3/envs/shortbred/bin/src/quantify_functions.py", line 256, in RunUSEARCH
"--maxrejects",str(iRejects),"--threads", str(iThreads)])
File "$path/miniconda3/envs/shortbred/lib/python2.7/subprocess.py", line 190, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['usearch', '--usearch_local', '$path/tmp/fasta.fna', '--db', '$path/tmp/card.fasta.udb', '--id', '80.0', '--userout', '$path/tmp/wgs_01out_01.out', '--userfields', 'query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits+ql+tl+qs+ts', '--maxaccepts', '1', '--maxrejects', '32', '--threads', '40']' returned non-zero exit status 1
I noticed the this topic:
https://forum.biobakery.org/t/non-printing-character-0x00-in-sequence-fasta-file-error/1956
I try many ways, paire files; single files; cat two files and transfer to fasta; fasta file with 60 line-width or no wrap per read. But all ways were showed the same as above. The file had processed with kneaddata, metaphlan and humann.