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cytham / nanovar

Structural variant caller for low-depth long-read sequencing data
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Workflow failing due to makeblastdb and hs-blastn #62

Closed lisosome closed 1 year ago

lisosome commented 1 year ago

Hi! I've been trying to run nanovar to detect SVs and CNVs from a low coverage run on minION. However, the workflows fails due to makeblastdb and, subsequently, hs-blastn. Nanovar (v1.4.1) has been installed via pip and the dependencies have been built following the instructions on the github page.

Here's the nanovar log: NanoVar-010823-1939.log

Here's the code I've been using: `inbam=$1 workdir=$2

module load conda samtools bedtools2 conda activate nanovar

minimap=/orfeo/cephfs/home/burlo/nardone/.conda/envs/minimap2/bin/minimap2 makeblastdb=/orfeo/cephfs/home/burlo/nardone/software/blast/ncbi-blast-2.3.0+/bin/makeblastdb hsblastn=/orfeo/cephfs/home/burlo/nardone/software/blast/queries/hs-blastn-src/v0.0.5/hs-blastn windowmsk=/orfeo/cephfs/home/burlo/nardone/software/blast/ncbi-blast-2.3.0+/bin/windowmasker

nanovar -x ont -t 24 -f hg38 --force --cnv hg38 --mm ${minimap} --mdb ${makeblastdb} --wmk ${windowmsk} --hsb ${hsblastn} ${inbam} /fast/burlo/fcrudele/resources/hgRef/GRCh38.p13/no_alt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna ${workdir}`

Thanks!

cytham commented 1 year ago

@lisosome Looks like you are missing the libnsl.so.1 shared library /orfeo/cephfs/home/burlo/nardone/software/blast/ncbi-blast-2.3.0+/bin/makeblastdb: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory You may want to look it up online to get the library.

Two things to note: 1) We are making some changes to the algorithm within NanoVar and will release a new version soon. This new version wouldn't need hsblastn so that would make things easier for you. You may want to wait for this version. 2) The --cnv option is still underdeveloped and I would not recommend using it. It will be temporary removed in the newer version until further notice. Meanwhile I would recommend you to use the the CNV workflow from https://github.com/epi2me-labs/wf-human-variation instead.

Thank you

lisosome commented 1 year ago

@cytham Thank you very much! Looks like I've missed that row reading the log file. I'm closing the issue.

Thanks again!