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konradjk / loftee

MIT License
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Can't exec "samtools" #98

Open jxcao98 opened 1 year ago

jxcao98 commented 1 year ago

Hi

Thanks for your nice tool!

I tried to run VEP by Singularity, but I got confused about where the path of Samtools should be placed.

I have added the path of Samtools to ~/.bashrc. However, I still got a warning, and It could appear multiple times.

Can't exec "samtools": No such file or directory at /home1/GENE_proc/tools/ensemblVEP/Plugin/LoF.pm line 539, <$fh> line 15248.
Use of uninitialized value $faidx in split at /home1/GENE_proc/tools/ensemblVEP/Plugin/LoF.pm line 540, <$fh> line 15248.
Can't exec "samtools": No such file or directory at /home1/GENE_proc/tools/ensemblVEP/Plugin/LoF.pm line 539, <$fh> line 85248.
Use of uninitialized value $faidx in split at /home1/GENE_proc/tools/ensemblVEP/Plugin/LoF.pm line 540, <$fh> line 85248.

The version of loftee:

[v.1.0.4](https://github.com/konradjk/loftee/releases/tag/v1.0.4_GRCh38)

The following is my script:

singularity exec $VepSif \
    vep \
    --cache --offline --force_overwrite \
    --dir $CacheVEP \
    --assembly GRCh38 \
    --fasta $referenceFastaVEP \
    --input_file $FilePath \
    --format vcf \
    -o stdout \
    --vcf \
    --stats_file $runDir/log/$ChrName.summary.html \
    --warning_file $runDir/log/$ChrName.warning.txt \
    --everything \
    --pick \
    --dir_plugins $PluginPath \
    --plugin dbNSFP,$PluginDataPath/dbnsfp/dbNSFP4.3a_grch38.gz,transcript_match=1,SIFT_pred,Polyphen2_HDIV_pred,Polyphen2_HVAR_pred,LRT_pred,MutationTaster_pred,CADD_phred,FATHMM_pred,MetaSVM_pred,REVEL_score,PROVEAN_pred,M-CAP_pred,PrimateAI_pred \
    --plugin LoF,loftee_path:$PluginPath,human_ancestor_fa:$PluginDataPath/loftee/human_ancestor.fa.gz,gerp_bigwig:$PluginDataPath/loftee/gerp_conservation_scores.homo_sapiens.GRCh38.bw,conservation_file:$PluginDataPath/loftee/loftee.sql \
    --plugin CADD,$PluginDataPath/cadd/GRCh38/whole_genome_SNVs.tsv.gz \
    --plugin Conservation,$PluginDataPath/conservation/gerp_conservation_scores.homo_sapiens.GRCh38.bw \
    | bgzip -c > $runDir/$ChrName.AnnotVEP.vcf.gz

It looked like VEP was not interrupted as I still got the final annotated files. So could I ignore these warnings safely?

Any suggestions are appreciated!

Best, Jixin

jon4thin commented 1 year ago

Jinxin, was there actually any LoFTEE annotations tho? It probably does not, if the package could not run (it needs samtools). The error says that VEP is looking for samtools at /home1/GENE_proc/tools/ensemblVEP/Plugin/LoF.pm

Make sure you can run samtools from your command line stand alone (try running a samtools command on a vcf).