Picard tools merge sam isssues ;;;;;;

[AnushaC]

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 .

[blancha]

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.