Hi all,
We have accumulated quite a lot of BAM files over the years and we would like (need) to archive the old(er) ones. We have tested CRAMtools 2.1 and we are very happy with the results. Since we are talking about thousands of BAM files, we cannot go without automation. But...
The problem is as followed:
- when I run CRAMtools in a job file, it terminates immediatly (throwing an exception).
- when I copy the command from the job file and execute it on the head node or on the node it previously failed on, I have no issues what so ever.
My job file looks like this:
The exception I get when submitting the job file to torque:
I have tried to include the full path to java to make sure the same version is used in all cases, but the problem remains.
Does anyone have an idea what could cause this problem and how I can fix it?
Many thanks,
Rick
We have accumulated quite a lot of BAM files over the years and we would like (need) to archive the old(er) ones. We have tested CRAMtools 2.1 and we are very happy with the results. Since we are talking about thousands of BAM files, we cannot go without automation. But...
The problem is as followed:
- when I run CRAMtools in a job file, it terminates immediatly (throwing an exception).
- when I copy the command from the job file and execute it on the head node or on the node it previously failed on, I have no issues what so ever.
My job file looks like this:
Code:
#PBS -N DNAXXXXXX #PBS -j oe #PBS -o /data/results/CRAM_archive/2013/october//DNAXXXXXX.log #PBS -r y #PBS -q bs_secondary #PBS -m ea #PBS -M [email protected] #PBS -l nodes=1:ppn=12 cp /data/results/BGI/DNAXXXXXX/DNAXXXXXX.bam /scratch/ cp /data/results/BGI/DNAXXXXXX/DNAXXXXXX.bam.bai /scratch/ java -jar /share/apps/cramtools-2.1.jar cram -I /data/results/BGI/DNAXXXXXX/DNAXXXXXX.bam -O /scratch/DNAXXXXXX.cram -R /data/references/GrCh37/GrCh37_reference.fa --preserve-read-names --capture-all-tags -L *8 java -cp /share/apps/cramtools-2.1.jar net.sf.cram.ValidateCramFile -I /scratch/DNAXXXXXX.cram -R /data/references/GrCh37/GrCh37_reference.fa mv /scratch/DNAXXXXXX.cram /data/results/CRAM_archive/2013/october// rm -f /scratch/DNAXXXXXX.bam rm -f /scratch/DNAXXXXXX.bam.bai
Code:
Exception in thread "main" java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at net.sf.cram.CramTools.invoke(CramTools.java:93) at net.sf.cram.CramTools.main(CramTools.java:123) Caused by: java.lang.RuntimeException: Uknown read or base category: 6 at net.sf.cram.lossy.QualityScorePreservation.parseSinglePolicy(QualityScorePreservation.java:155) at net.sf.cram.lossy.QualityScorePreservation.parsePolicies(QualityScorePreservation.java:79) at net.sf.cram.lossy.QualityScorePreservation.<init>(QualityScorePreservation.java:39) at net.sf.cram.Bam2Cram.main(Bam2Cram.java:273) ... 6 more
Does anyone have an idea what could cause this problem and how I can fix it?
Many thanks,
Rick
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