error for virus_pathogen_database.mmi

[tulikasriv26]

I am continously getting this error for paired -ended files
Processing sample: BBW_0513_FS_CKDL240028581-1A_22FWVLLT4_L4
Time Update: Starting main bash script for EsViritu General Mode @ 10-02-24---23:16:26
can't find minimap2 index for pipeline. should be: /home/tulika.bhardwaj/miniconda3/envs/EsViritu/lib/python3.12/site-packages/EsViritu/virus_pathogen_database.mmi
exiting
/home/............/miniconda3/envs/EsViritu/lib/python3.12/site-packages/EsViritu
2 paired read files
DB: /home/............./miniconda3/envs/EsViritu/lib/python3.12/site-packages/EsViritu
filter seqs: /........../lib/python3.12/site-packages/EsViritu
version 0.2.3
0
coverm found
minimap2 found
samtools found
bioawk found
seqkit found
bedtools found
fastp found
seqfu found

And this is the script
raw="/work/ebg_lab/gm/wastewater_data/usftp21.novogene.com/01.RawData/EsViritu"
out="/work/ebg_lab/gm/wastewater_data/usftp21.novogene.com/01.RawData/EsViritu_result"

#####################################################################################################
conda env config vars set ESVIRITU_DB=/work/ebg_lab/gm/wastewater_data/usftp21.novogene.com/01.RawData/EsViritu/DBs/v2.0.2
mkdir -p $out
while read p
do
echo "Processing sample: $p"
EsViritu -r $raw/${p}_1.fq $raw/${p}_2.fq -s ${p} -t 16 -o $out/$p -p paired
done < list

[mtisza1]

Hi, thanks for opening the issue.

This may or may not have changed in recent conda updates, but any time I use the command: conda env config vars set, it prompts me to deactivate/reactivate the environment for this change to take effect. So, I think that's your problem.

In your case, you can simply use the --db flag in your EsViritu command, e.g.:

--db /work/ebg_lab/gm/wastewater_data/usftp21.novogene.com/01.RawData/EsViritu/DBs/v2.0.2

Let me know if this helps.

Best,

Mike

[tulikasriv26]

Thanks for your reply. I must try your suggestions and will let you know.

…

On Wed, Oct 9, 2024 at 11:35 AM Mike Tisza ***@***.***> wrote: Hi, thanks for opening the issue. This may or may not have changed in recent conda updates, but any time I use the command: conda env config vars set, it prompts me to deactivate/reactivate the environment for this change to take effect. So, I think that's your problem. In your case, you can simply use the --db flag in your EsViritu command, e.g.: --db /work/ebg_lab/gm/wastewater_data/ usftp21.novogene.com/01.RawData/EsViritu/DBs/v2.0.2 Let me know if this helps. Best, Mike — Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AINHNVEXEODOCBWP45LSOE3Z2VSOXAVCNFSM6AAAAABPJAVYS2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBSHEYTAMRSGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[tulikasriv26]

i am facing some new issue while following your suggestion [M::worker_pipeline::65100.971*15.49] mapped 333334 sequences [2024-10-09T23:15:29Z ERROR coverm::bam_generator] The STDERR for the samtools sort part was: samtools sort: failed writing to "/tmp/coverm_fifo.mMCAlvTztJmh/coverm-make-samtools-sortlmOtNP.0020.bam": No such file or directory [2024-10-09T23:15:29Z ERROR coverm::bam_generator] The STDERR for the samtools view for cache part was: [main_samview] fail to read the header from "-". [2024-10-09T23:15:29Z ERROR coverm::bam_generator] The STDERR for the remove_minimap2_duplicated_headers part was: thread 'main' panicked at 'failed printing to stdout: Broken pipe (os error 32)', library/std/src/io/stdio.rs:1008:9 note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace [2024-10-09T23:15:29Z ERROR coverm::bam_generator] Cannot continue since mapping failed. On Wed, Oct 9, 2024 at 12:44 PM Tulika Bhardwaj ***@***.***> wrote:

…

Thanks for your reply. I must try your suggestions and will let you know. On Wed, Oct 9, 2024 at 11:35 AM Mike Tisza ***@***.***> wrote: > Hi, thanks for opening the issue. > > This may or may not have changed in recent conda updates, but any time I > use the command: conda env config vars set, it prompts me to > deactivate/reactivate the environment for this change to take effect. So, I > think that's your problem. > > In your case, you can simply use the --db flag in your EsViritu command, > e.g.: > > --db /work/ebg_lab/gm/wastewater_data/ > usftp21.novogene.com/01.RawData/EsViritu/DBs/v2.0.2 > > Let me know if this helps. > > Best, > > Mike > > — > Reply to this email directly, view it on GitHub > <#12 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AINHNVEXEODOCBWP45LSOE3Z2VSOXAVCNFSM6AAAAABPJAVYS2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBSHEYTAMRSGI> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[mtisza1]

Hi,

This looks like a coverm error. It seems due to the /tmp directory not existing. There's a way to go around this and set an alternative tmp path:

https://wwood.github.io/CoverM/coverm-genome.html#frequently-asked-questions-faq

Alternatively, it's possible your computer/node is running out of RAM. You can sample down your files with seqkit head or a similar command to check this.

Mike