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, 16:40, 22 October 2014
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| 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 |
− | and should see the following subdirectories under the user specified output directory:
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− | * bams/
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− | * Makefiles/
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− | * QCFiles/ (if all quality control is not disabled)
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− | * tmp/
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− | 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. |
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| + | === 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 |
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| + | You should also see a <code>.OK</code> for each Sample in the index file. |
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| 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. |
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− | On success, the bams/ directory contains the final BAMs and bais. | + | '''On success, the bams/ directory contains the final BAMs and bais.''' |
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− | If processing fails part way through, you can pick up where you left off by rerunning gotcloud or the make command.
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