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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.
On success, the bams/ directory contains the final BAMs, bais, and md5s.
On success, the bams/ directory contains the final BAMs and bais.
If processing fails part way through, you can pick up where you left off by rerunning gotcloud or the make command.
If processing fails part way through, you can pick up where you left off by rerunning gotcloud or the make command.
