Question: Question: Viromescan tool for metagenomics analysis:Failed to find bmfilter
1
gravatar for 1558105383
13 months ago by
155810538310
155810538310 wrote:

Annotate the metagenome sample with virus and use Viromescan tool, I was working on Viromescan tool with the manual. However, I stuck with a problem related to bmfilter.I enter the following command:

Blockquote $./viromescan -p 8 -m /mnt/data5/sunzheng/tools/ -d virus_ALL -1 /mnt/data5/sunzheng/lim/megahit/B70_paired_1.fastq.gz -2 /mnt/data5/sunzheng/lim/megahit/B70_paired_2.fastq.gz -o viromescan_B70

There was such a mistake:

Blockquote 22272467 reads; of these: 22272467 (100.00%) were paired; of these: 22272367 (100.00%) aligned concordantly 0 times 5 (0.00%) aligned concordantly exactly 1 time 95 (0.00%) aligned concordantly >1 times ---- 22272367 pairs aligned concordantly 0 times; of these: 1 (0.00%) aligned discordantly 1 time ---- 22272366 pairs aligned 0 times concordantly or discordantly; of these: 44544732 mates make up the pairs; of these: 44544196 (100.00%) aligned 0 times 141 (0.00%) aligned exactly 1 time 395 (0.00%) aligned >1 times 0.00% overall alignment rate Info: no ./bmtagger.conf found Using following programs: which: no bmfilter in (/mnt/data5/sunzheng/tools/viromescan/viromescan.sh:/mnt/data6/sunzheng/tools/parallel-20191022/parallel:/home/gene/sunzheng/miniconda2/bin:/home/gene/sunzheng/miniconda2/condabin:/home/gene/sunzheng/tools/MetaCLADE-1.1-190320:/home/gene/sunzheng/tools/dbcan/run_dbcan-master/hmmscan-parser:/home/gene/sunzheng/tools/bracken/Bracken-master:/home/gene/sunzheng/tools/bracken/kraken2:/mnt/data6/sunzheng/tools/Python_3.7.4/bin:/home/gene/sunzheng/shotgun_taxonomic_classifier/MetaPhlAn2/metaphlan2:/home/gene/sunzheng/shotgun_taxonomic_classifier/MetaPhlAn2/metaphlan2/utils:/home/gene/sunzheng/tools/qiime-1.9.0/chimeraslayer-4.29.2010-release/ChimeraSlayer:/home/gene/sunzheng/tools/qiime-1.9.0/chimeraslayer-4.29.2010-release/NAST-iEr:/home/gene/sunzheng/tools/qiime-1.9.0/cytoscape-2.7.0-release:/home/gene/sunzheng/tools/qiime-1.9.0/blast-2.2.22-release/bin:/home/gene/sunzheng/tools/qiime-1.9.0/rdpclassifier-2.2-release:/home/gene/sunzheng/tools/qiime-1.9.0/infernal-1.0.2-release/bin:/home/gene/sunzheng/tools/qiime-1.9.0/cdhit-3.1-release:/home/gene/sunzheng/tools/qiime-1.9.0/mothur-1.25.0-release:/home/gene/sunzheng/tools/qiime-1.9.0/muscle-3.8.31-release:/home/gene/sunzheng/tools/qiime-1.9.0/SeqPrep-v1.1-release:/home/gene/sunzheng/tools/qiime-1.9.0/bwa-0.6.2-release:/home/gene/sunzheng/tools/qiime-1.9.0/qiime-galaxy-0.0.1-repository-c2814c3c/scripts:/home/gene/sunzheng/tools/qiime-1.9.0/vienna-1.8.4-release:/home/gene/sunzheng/tools/qiime-1.9.0/drisee-1.2-release:/home/gene/sunzheng/tools/qiime-1.9.0/sourcetracker-0.9.5-release:/home/gene/sunzheng/tools/qiime-1.9.0/raxml-7.3.0-release:/home/gene/sunzheng/tools/qiime-1.9.0/rtax-0.984-release:/home/gene/sunzheng/tools/qiime-1.9.0/cdbtools-10.11.2010-release:/home/gene/sunzheng/tools/qiime-1.9.0/blat-34-release:/home/gene/sunzheng/tools/qiime-1.9.0/clearcut-1.0.9-release:/opt/tools/dynamic-meta-storms/bin:/opt/tools/Meta-Storms/bin:/opt/tools/parallel-meta/bin:/usr/loacal/anaconda2/bin:/opt/tools/samtools/bin:/opt/tools/perl/bin:/opt/tools/ncbi-blast-2.6.0+/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/bin:/usr/bin:/usr/local/bin:/usr/local/python3/bin:/opt/tools/meta-tools/bin:/opt/tools/parallel-meta/Rscript:/opt/tools/meta-tools/Rscrpit:/home/gene/sunzheng/tools/bowtie2-2.2.4:/home/gene/sunzheng/tools/idba-1.1.1/bin:/opt/tools/parallel-meta/bin:/home/gene/sunzheng/tools/MetaGeneMark_linux_64/mgm:/home/gene/sunzheng/tools/cd-hit-v4.6.1-2012-08-27:/home/gene/sunzheng/tools/samtools-1.1:/home/gene/sunzheng/tools/ncbi-blast-2.2.30+/binsource:/home/gene/sunzheng/tools/qiime-1.9.0/activate.sh:/home/gene/sunzheng/shotgun_taxonomic_classifier/Kraken/kraken-0.10.5-beta:/home/gene/sunzheng/shotgun_taxonomic_classifier/Kraken/kraken-0.10.5-beta/jellyfish-1.1.11:/home/gene/sunzheng/shotgun_taxonomic_classifier/Centrifuge/centrifuge-1.0.3-beta:/home/gene/sunzheng/shotgun_taxonomic_classifier/Kraken/kraken-0.10.5-beta/jellyfish-1.1.11/bin:/home/gene/sunzheng/shotgun_taxonomic_classifier/Centrifuge/centrifuge-1.0.3-beta:/home/gene/sunzheng/Home_database/16SPIP/16sPIP-master/bin:/home/gene/sunzheng/shotgun_taxonomic_classifier/MOCAT/MOCAT/src:/home/gene/sunzheng/shotgun_taxonomic_classifier/MOCAT/MOCAT/src:/home/gene/sunzheng/shotgun_taxonomic_classifier/bowtie2-2.3.2:6sPIP_PATH:6sPIP_BIN:/mnt/data6/sunzheng/tools/meta-storms/bin:/opt/tools/parallel-meta/bin:/opt/tools/GPU-Meta-Storms/bin:/home/gene/sunzheng/shotgun_taxonomic_classifier/MOCAT/MOCAT/src:/home/gene/sunzheng/shotgun_taxonomic_classifier/MOCAT/MOCAT/src=/mnt/data5/sunzheng/tools/viromescan/tools/bmfilter) FATAL: Failed to find bmfilter

Has anyone ever encountered such a problem?Can anyone give some direction?

software error • 348 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 13 months ago by 155810538310
1

I think you haven't performed the installation correctly. bmfilter is missing from this location: mnt/data5/sunzheng/tools/viromescan/tools/bmfilter

and the instructions say:

If you downloaded Bmtools, you will have to move bmtagger.sh, bmfilter, bmtool, extract_fullseq and srprism scripts in the directory $PWD/viromescan/tools inside the viromescan folder.

ADD REPLYlink written 13 months ago by Mark860

First of all, thank you for your reply. I have downloaded bmtools compression package and bmfilter compression package in src folder from ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger website, and moved relevant scripts to /MNT/DATA5/Sun Zheng/Tools/Viromescan/Tools; I also added bmfilter to the environment variable, but there was still an error: Failed to find bmfilter.

ADD REPLYlink written 13 months ago by 155810538310

No idea sorry! Try contacting the developers.

ADD REPLYlink written 13 months ago by Mark860
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