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

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, 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 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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