nhmmer failed to run - Parse failed

[cliffbueno]

Hello,

Thanks for a great tool! I'm using phyloFlash 3.4.2. I was trying to make a custom database with ITS sequences. I followed the directions in section 4.3 here https://hrgv.github.io/phyloFlash/install.html to properly format my fasta file with the sequences. I then ran the phyloFlash_makedb.pl command with 16 CPUs, supplying my fasta and the univec file.

phyloFlash_makedb.pl --ref_minlength 130 --CPUs 16 --mem 10 --silva_file /scratch/alpine/clbd1748/Australia_copy/SILVA_CustomDB_ITS.fasta --univec_file /scratch/alpine/clbd1748/UniVec

It looks like the program first confirmed that the software was present, and then started barnnap, but then there was a "nhmmer failed to run - Parse failed" error. Below are the contents of the"phyloFlash_log_on_error" file and the "tmp.barrnap_hits.bac.barrnap.out" log file. Thank you for any troubleshooting suggestions or workarounds.

phyloFlash_log_on_error:
[13:07:27] Checking for required tools.
[13:07:27] Using vsearch found at
"/projects/clbd1748/software/anaconda/envs/pf/bin/vsearch".
[13:07:27] Using bbmap found at
"/projects/clbd1748/software/anaconda/envs/pf/bin/bbmap.sh".
[13:07:27] Using grep found at "/usr/bin/grep".
[13:07:27] Using barrnapHGV found at
"/projects/clbd1748/software/anaconda/envs/pf/lib/phyloFlash/barrnap-HGV/bin/barrnap_HGV".
[13:07:27] Using bbduk found at
"/projects/clbd1748/software/anaconda/envs/pf/bin/bbduk.sh".
[13:07:27] Using bbmask found at
"/projects/clbd1748/software/anaconda/envs/pf/bin/bbmask.sh".
[13:07:27] Using bowtiebuild found at
"/projects/clbd1748/software/anaconda/envs/pf/bin/bowtie-build".
[13:07:27] All required tools found.
[13:07:27] using local copy of univec: /scratch/alpine/clbd1748/UniVec
[13:07:27] using local copy of Silva SSU RefNR:
/scratch/alpine/clbd1748/Australia_copy/SILVA_CustomDB_ITS.fasta
[13:07:27] unpacking SILVA database
[13:07:27] searching for LSU contamination in SSU RefNR
[13:07:27] running subcommand:
/projects/clbd1748/software/anaconda/envs/pf/lib/phyloFlash/barrnap-HGV/bin/barrnap_HGV
--kingdom bac --threads 16 --evalue 1e-10 --gene lsu --reject
0.01 ./CustomDB/SILVA_SSU.fasta >tmp.barrnap_hits.bac.gff
2>tmp.barrnap_hits.bac.barrnap.out
[13:07:28] FATAL: Tool execution failed!.
Error was 'No such file or directory' and return code '512'
Check log file tmp.barrnap_hits.bac.gff
Check error log file tmp.barrnap_hits.bac.barrnap.out
Aborting.
[13:07:28] Saving log to file phyloFlash_log_on_error

tmp.barrnap_hits.bac.barrnap.out:
[13:07:27] This is barrnap_HGV 0.7
[13:07:27] Written by Torsten Seemann torsten.seemann@gmail.com
[13:07:27] Obtained from https://github.com/Victorian-Bioinformatics-Consortium/barrnap
[13:07:27] Detected operating system: linux
[13:07:27] Using HMMER binary: /projects/clbd1748/software/anaconda/envs/pf/lib/phyloFlash/barrnap-HGV/bin/../binaries/linux/nhmmer
[13:07:27] Will use 16 threads
[13:07:27] Setting evalue cutoff to 1e-10
[13:07:27] Will tag genes < 0.8 of expected length.
[13:07:27] Will reject genes < 0.01 of expected length.
[13:07:27] Using database: /projects/clbd1748/software/anaconda/envs/pf/lib/phyloFlash/barrnap-HGV/bin/../db/lsu/bac.hmm
[13:07:27] Scanning ./CustomDB/SILVA_SSU.fasta for lsu bac rRNA genes... please wait
[13:07:27] Command: /projects/clbd1748/software/anaconda/envs/pf/lib/phyloFlash/barrnap-HGV/bin/../binaries/linux/nhmmer --cpu 16 -E 1e-10 --w_length 3878 -o /dev/null --tblout /dev/stdout /projects/clbd1748/software/anaconda/envs/pf/lib/phyloFlash/barrnap-HGV/bin/../db/lsu/bac.hmm ./CustomDB/SILVA_SSU.fasta
[13:07:28] nhmmer failed to run - Parse failed (sequence file ./CustomDB/SILVA_SSU.fasta):