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Old 07-31-2012, 11:45 PM   #29
Location: beijing

Join Date: Jul 2012
Posts: 33
Default a unusual problem in FREEC

I meet an unusual problem when I run FREEC. If I provide a mateCopyNumberFile, and then qsub, it will run sucessfully, but in fact I normally don't have mateCopyNumberFile, but if I don't provide it, it can't run, the error message is:

sh:samtools:command not found

Error: FREEC was not able to extract reads from /database/chenxi/task/cancerProgram/pipline/bwa/BPMICS4/sortedbam/PD1W_XXL_BPMICS4_NoIndex_modified.bam

Check your parameters: inputFormat and matesOrientation
Use "matesOrientation=0" if you have single end reads
Check the list of possible input formats at

I can't figure out what happens here. My parameters are absolutely correct, and I have samtools in my working directory and environmental PATH.

Can anyone give me some helps? I am not able to run FREEC because of this.
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