# FIX: metaphlan4 bowtie2-build --threads flag bug #229 **URL:** \ **Category:** Feature/Pull Request\ **Created:** [August 22, 2024, 5:37pm UTC](https://forum.biobakery.org/t/fix-metaphlan4-bowtie2-build-threads-flag-bug-229/7395 "2024-08-22T17:37:43Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![heloint](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/heloint/32/2986_2.png) [@heloint](https://forum.biobakery.org/u/heloint)\ **Post date:** [August 22, 2024, 5:37pm UTC](https://forum.biobakery.org/t/fix-metaphlan4-bowtie2-build-threads-flag-bug-229/7395/1 "2024-08-22T17:37:43Z")
# metaphlan4 bowtie2-build “–threads” flag bug ## Software details **metaphlan4 version:** _MetaPhlAn version 4.1.1 (11 Mar 2024)_ **bowtie2-build version:** _bowtie2-build version 2.2.3 64-bit, compiled with gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)_ * * * ## Issue **Traceback output** ```bash bowtie2-build: unrecognized option '--threads' Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2-build [options]* reference_in comma-separated list of files with ref sequences bt2_index_base write bt2 data to files with this dir/basename ***Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes.*** Options: -f reference files are Fasta (default) -c reference sequences given on cmd line (as ) --large-index force generated index to be 'large', even if ref has fewer than 4 billion nucleotides -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting -p/--packed use packed strings internally; slower, less memory --bmax max bucket sz for blockwise suffix-array builder --bmaxdivn max bucket sz as divisor of ref len (default: 4) --dcv diff-cover period for blockwise (default: 1024) --nodc disable diff-cover (algorithm becomes quadratic) -r/--noref don't build .3/.4 index files -3/--justref just build .3/.4 index files -o/--offrate SA is sampled every 2^ BWT chars (default: 5) -t/--ftabchars # of chars consumed in initial lookup (default: 10) --seed seed for random number generator -q/--quiet verbose output (for debugging) -h/--help print detailed description of tool and its options --usage print this usage message --version print version information and quit Error: Encountered internal Bowtie 2 exception (#1) Command: bowtie2-build --wrapper basic-0 -q /tmp/tmpm62vnjcr/v_mks.fa /tmp/tmpm62vnjcr/v_mks --threads 4 Traceback (most recent call last): File "/usr/local/bin/metaphlan", line 8, in sys.exit(main()) File "/usr/local/lib/python3.10/site-packages/metaphlan/metaphlan.py", line 1529, in main VSC_report = vsc_bowtie2(viralTempFolder, pars['nproc'], file_format=pars['input_type'], File "/usr/local/lib/python3.10/site-packages/metaphlan/metaphlan.py", line 450, in vsc_bowtie2 subp.check_call( [bt2build_call, markerfile, dbpath, '-q','--threads', str(nproc)] ) File "/usr/local/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['bowtie2-build', '/tmp/tmpm62vnjcr/v_mks.fa', '/tmp/tmpm62vnjcr/v_mks', '-q', '--threads', '4']' returned non-zero exit status 1. ``` In the “./metaphlan/metaphlan.py” file, on line 445, in the subprocess call, the script calls the **“bowtie2-build”** command with the flag **“–threads”** to enable multithreading/multiprocessing. The “–threads” doesn’t exists, rather the correct switch for multi-cores seems to be **“-p”**. It’s probably a case of poor documentation, as of the current **“–help”** flag gives the following output: ```bash Bowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2-build [options]* reference_in comma-separated list of files with ref sequences bt2_index_base write bt2 data to files with this dir/basename ***Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes.*** Options: -f reference files are Fasta (default) -c reference sequences given on cmd line (as ) --large-index force generated index to be 'large', even if ref has fewer than 4 billion nucleotides -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting -p/--packed use packed strings internally; slower, less memory --bmax max bucket sz for blockwise suffix-array builder --bmaxdivn max bucket sz as divisor of ref len (default: 4) --dcv diff-cover period for blockwise (default: 1024) --nodc disable diff-cover (algorithm becomes quadratic) -r/--noref don't build .3/.4 index files -3/--justref just build .3/.4 index files -o/--offrate SA is sampled every 2^ BWT chars (default: 5) -t/--ftabchars # of chars consumed in initial lookup (default: 10) --seed seed for random number generator -q/--quiet verbose output (for debugging) -h/--help print detailed description of tool and its options --usage print this usage message --version print version information and quit ``` * * * ## Command to reproduce ```bash metaphlan \ --bowtie2db /gpfs/projects/bsc40/current/okhannous/Metaphlan4/db \ --index mpa_vJun23_CHOCOPhlAnSGB_202307 /gpfs/projects/bsc40/current/dmajer/metaline-testy-output/BAM/corachan.unmapped.fastq.gz \ --input_type fastq \ --bowtie2out /gpfs/projects/bsc40/current/dmajer/metaline-testy-output/METAPHLAN4/corachan.bz2 -s /gpfs/projects/bsc40/current/dmajer/metaline-testy-output/METAPHLAN4/corachansam.bz2 \ --profile_vsc -o /gpfs/projects/bsc40/current/dmajer/metaline-testy-output/METAPHLAN4/corachan_profiled.txt \ --nproc 4 \ --vsc_out /gpfs/projects/bsc40/current/dmajer/metaline-testy-output/METAPHLAN4/corachan.vsc.txt ``` * * * ## Submitted fix Substitute line 445 in ./metaphlan/metaphlan.py **FROM** : ```python subp.check_call( [bt2build_call, markerfile, dbpath, '-q','--threads', str(nproc)] ) ``` **TO:** ```python try: subp.check_call([bt2build_call, markerfile, dbpath, '-q','--threads', str(nproc)]) except subp.CalledProcessError as e: print(e, file=sys.stderr) errored_cmd = " ".join([bt2build_call, markerfile, dbpath, '-q','--threads', str(nproc)]) corrected_cmd = " ".join([bt2build_call, markerfile, dbpath, '-q','-p', str(nproc)]) print( f"==> WARNING: '{errored_cmd}' command is incompatible with the " "current version of bowtie2-build. " f"Re-trying the process with '{corrected_cmd}'", file=sys.stderr ) subp.check_call([bt2build_call, markerfile, dbpath, '-q','-p', str(nproc)]) ``` _If the “–threads” flag was used, then at some point it was working correctly with older versions of Bowtie2. This way there’s backwards compatibility._