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IARCbioinfo / needlestack

Multi-sample somatic variant caller
GNU General Public License v3.0
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Failed to open file #191

Closed theo-allnutt-bioinformatics closed 2 years ago

theo-allnutt-bioinformatics commented 3 years ago

Hi, getting this error.. not sure why.

Thanks,

needlestack.sh --ref=79900cent.fa --bam_folder=bam/ --output_vcf=needle.vcf --use_file_name

NEEDLESTACK v1.1: A MULTI-SAMPLE SOMATIC VARIANT CALLER

Copyright (C) 2017 IARC/WHO This program comes with ABSOLUTELY NO WARRANTY; for details see LICENSE.txt This is free software, and you are welcome to redistribute it under certain conditions; see LICENSE.txt for details.

Mandatory arguments: Reference in fasta format (--ref) : 79900cent.fa Input BAM folder (--bam_folder) : bam/ output vcf (--output_vcf) : needle.vcf Options: output folder (--output_folder) : Intervals for calling (--region) : Perform a tumor-normal somatic variant calling (--tn_pairs) : no To consider a site for calling: minimum median coverage (--min_dp) : 30 minimum of alternative reads (--min_ao) : 3 Phred-scale qvalue threshold (--min_qval) : 50 Strand bias measure (--sb_type) : SOR Strand bias threshold for SNVs (--sb_snv) : 100 Strand bias threshold for indels (--sb_indel) : 100 Minimum allelic fraction for power computations (--power_min_af): -1 Sigma parameter for germline (--sigma) : 0.1 Samtools minimum mapping quality (--map_qual) : 0 Samtools minimum base quality (--base_qual) : 13 Samtools maximum coverage before downsampling (--max_dp) : 50000 Sample names definition (--use_file_name) : FILE PDF regression plots (--plots) : ALL Flags: Alignment plots (--do_alignments) : no Labeling outliers in regression plots (--no_labels) : yes Add contours in plots and plot min(AF)~DP (--no_contours) : yes Output all SNVs (--all_SNVs) : no Perform an extra-robust regression (--extra_robust_gl) : no Skip indels (--no_indels) : no

WARNING : minimum allelic fraction for power computations must be in [0,1] (--power_min_af) [warning] samtools mpileup option L is functional, but deprecated. Please switch to using bcftools mpileup in future. [E::hts_open_format] Failed to open file A00119:345:HY7KVDRXX:1:2119:2347:35243:0-150 [mpileup] failed to open A00119:345:HY7KVDRXX:1:2119:2347:35243:0-150: Protocol not supported [1] "2021-06-07 16:16:38 AEST" [1] 0.2 [1] "2021-06-07 16:16:40 AEST" mv: cannot stat '*.pdf': No such file or directory

mfoll commented 3 years ago

Hi,

I suspect there is an issue with the file names when I see this: [mpileup] failed to open A00119:345:HY7KVDRXX:1:2119:2347:35243:0-150: Protocol not supported Maybe check with a toy example renaming your files to see if this is the issue?

theo-allnutt-bioinformatics commented 3 years ago

File names are ok. That's a read name, not a file, which is what I don't understand. Thanks.

mfoll commented 3 years ago

Oh right, then I guess this is a samtools related issue. Maybe try to manually run the command on a few BAM files to isolate the issue, it is here in the code: samtools mpileup --fasta-ref $fasta_ref --region $region --ignore-RG --min-BQ $base_qual --min-MQ $map_qual --max-idepth 1000000 --max-depth $max_dp $bam_folder*.bam https://github.com/IARCbioinfo/needlestack/blob/master/bin/needlestack.sh#L477