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Revision as of 16:40, 22 October 2014
, 16:40, 22 October 2014→Running the Alignment Pipeline
On success, you will see:
On success, you will see:
Processing finished in nn secs with no errors reported
Processing finished in nn secs with no errors reported
You should see a <code>.OK</code> for each Sample in the index file.
If processing fails part way through, you can pick up where you left off by rerunning gotcloud or the make command.
=== Alignment Pipeline Output ===
Upon successful completion of the alignment pipeline, you should see the following files/ subdirectories under the user specified output directory:
* '''bam.list''' - file containing sample -> BAM mapping that can be used in other GotCloud pipelines
* '''bams/''' - contains the final BAM and bai (BAM index) files
** '''*.recal.bam'''
** '''*.recal.bam.bai'''
** ''*.recal.bam.bai.done'' - temp file indicating this step completed successfully
** ''*.recal.bam.done'' - temp file indicating this step completed successfully
** *.recal.bam.metrics - dedup & recalibration log
** *.recal.bam.qemp - recalibration tables
* Makefiles/ - contains the Makefiles and logs used by GotCloud to run the alignment pipeline
* '''QCFiles/''' - contains quality control results if quality control is not disabled
**
* tmp/ - contains intermediate files (most are deleted unless --keepTmp is specified)
* *.OK - one OK file per sample; indicates the Sample successfully completed alignment
You should also see a <code>.OK</code> for each Sample in the index file.
If you do not see these <code>.OK</code> files, then your Alignment Pipeline failed.
If you do not see these <code>.OK</code> files, then your Alignment Pipeline failed.
On success, the bams/ directory contains the final BAMs and bais.
'''On success, the bams/ directory contains the final BAMs and bais.'''
