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  • Picard tools merge sam isssues ;;;;;;

    Hi All,
    I am trying to use merge sam with script so that I can automate this for several tissues . Command is working when I am giving this in command line
    ################################################
    !/bin/bash

    FILES=''

    for file in $(find /raid/development/anusha/DGFDATA_Tissue_DATA/brain -name \*.sorted.bam)
    do
    FILES="$FILES $file"

    done
    #echo $FILES

    java -Xmx2g -jar /raid/software/src/picard-tools-1.53/MergeSamFiles.jar I=$FILESO=/raid/development/anusha/DGFDATA_Tissue_DATA/brain/brain.merge.bam AS=FALSE USE_THREADING=TRUE VALIDATION_STRINGENCY=SILENT&
    #############################################
    anusha@cn1:/raid/development/anusha/DGFDATA_Tissue_DATA> echo $FILES

    /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203405.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203400.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203406.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203407.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203408.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203404.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203401.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203402.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203403.sorted.bam /raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203409.sorted.bam

    ###########################################

    ERROR: Invalid argument '/raid/development/anusha/DGFDATA_Tissue_DATA/brain/SRR203400.sorted.bam'

    Merges multiple SAM/BAM files into one file.
    ######################################
    I am getting error like this

    Hope to help on this . Thanks in advance .

  • #2
    For one thing, you're missing a space in your script, as you pasted it.

    I=$FILESO=/raid/development/anusha/DGFDATA_Tissue_DATA/brain/brain.merge.bam

    ---

    Additional comments.

    Picard-tools 1.53 dates back to 2011.
    The current version is Picard-tools 1.114.

    I find Python scripts easier to read, and maintain, but perhaps bash is appropriate for such a short script.
    Last edited by blancha; 06-10-2014, 11:05 PM.

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