minimap2 --version Segmentation fault

[jayramr]

Hello,

I installed squeezemeta v1.6.3 and tried to download the database as per below command

perl /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3/SqueezeMeta/utils/install_utils/download_databases.pl /scratch/Reference_Genomes/In_house/Metagenomic/squeezemeta/

I got below error during the final stage.

I ran this installation via mamba.

Checking that all the required R libraries are available in this environment
        R -h OK
        R -e 'library(doMC)' OK
        R -e 'library(ggplot2)' OK
        R -e 'library(data.table)' OK
        R -e 'library(reshape2)' OK
        R -e 'library(pathview)' OK
        R -e 'library(DASTool)' OK
        R -e 'library(SQMtools)' OK

Checking binaries
        spades.py OK
        metabat2 OK
        jgi_summarize_bam_contig_depths OK
        samtools OK
        bwa OK
sh: line 1: 2821373 Segmentation fault      /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3/SqueezeMeta/bin/minimap2 --version > /dev/null 2>&1
        minimap2 NOT OK
                ERROR: Error running /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3/SqueezeMeta/bin/minimap2 --version
        diamond OK
        hmmsearch OK
        cd-hit-est OK
        kmer-db OK
        aragorn OK
        mothur OK

Checking that SqueezeMeta is properly configured... checking database in /scratch/Reference_Genomes/In_house/Metagenomic/squeezemeta/db
        nr.db OK
        CheckM manifest OK
        LCA_tax DB OK

------------------------------------------------------------------------------

WARNING: Some SqueezeMeta dependencies could not be found in your environment or failed to execute!
        - ERROR: Error running /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3/SqueezeMeta/bin/minimap2 --version

Please advise how to fix this minimap segfault error.

[fpusan]

What OS/distro and version are you using? To fix, try the following: 1) Install a valid minimap2 version using conda mamba install -c bioconda minimap2 2) Edit the file /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3/SqueezeMeta/scripts/SqueezeMeta_conf.pl 3) Change the value of the variable $minimap2_soft to just minimap2. The line should now read $minimap2_soft = "minimap2"; 4) Run test_install.pl to check whether the issue was fixed

[jayramr]

OS - RHEL8

I tried to resintall everything from the scratch as follows:-

mamba create -p /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3 -c conda-forge -c bioconda -c anaconda -c fpusan squeezemeta=1.6.3
mamba activate activate /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3

perl /scratch/gencore/conda3/envs/SqueezeMeta-1-6-3/SqueezeMeta/utils/install_utils/configure_nodb.pl <path-to-db>
test_install.pl

All the checks were passed and there is no minimap error came this time.

Not sure why this minimap2 segfault error came before. There is no package minimap2 installed at this time.

Thanks for your help.

[fpusan]

I wonder why it happened, but it is good news that reinstalling the current version seemed to fix the issue. Thanks for reporting!