Could not find or load main class net.sf.picard.sam.SortSam

Question

[blur]

Hi,

I am trying to run a protocol from a paper in nature, and I am stuck with this step: The commands parameters are as described in the paper, but I get an error msg "Error: Could not find or load main class net.sf.picard.sam.SortSam"

anyone have any idea what I am doing wrong?

java -Xmx2048m -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Djava.io.tmpdir=/nadata/users/me/ -cp /nadata/software/GATK_3.6/GenomeAnalysisTK.jar net.sf.picard.sam.SortSam INPUT=/nadata/users/me/B_RBFOX2_R1.fastq.adaptorTrim_round2_rmRep_reDup.bam TMP_DIR=/nadata/users/me/ OUTPUT=/nadata/users/mor/ECLIP/RBFOX2/B_RBFOX2_R1.fastq.adaptorTrim_round2_rmRep_reDup_sorted.bam VALIDATION_STRINGENCY=SILENT SO=coordinate CREATE_INDEX=true
    Error: Could not find or load main class net.sf.picard.sam.SortSam

Thanks!

[venu]

It would be helpful if you also post the link to the paper and in which section it is described. (BTW, it is just a typo here right? ava insetad of java)

[blur]

yeah, that was a typo... it is taken from this paper: Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP) http://www.nature.com/nmeth/journal/v13/n6/full/nmeth.3810.html from Nature

Answer 1

[Pierre Lindenbaum]

there is no such net.sf.picard.sam.SortSam in GATK (tested with 3.7)

   $  jar tvf GenomeAnalysisTK.jar | grep SortSam

SortSam is not part of the package net.sf.picard.sam since a long time: https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/sam/SortSam.java (but picard.sam )

what you want is not GATK but picard : https://github.com/broadinstitute/picard/releases/tag/2.9.2

java -jar picard.jar SortSam

furthermore, samtools sort is faster

[blur]

I tried substituting the link to GATK with a link to Picard but it didn't work... I also did samtools sort, and it worked like charm, but I'd still like to know why this didn't work...