Failure to check exit codes of run_command causes a hang

[pshaughn]

extract.py calls run_command repeatedly and assumes each execution has succeeded, without checking error codes. When samtools fails at one step, this can result in the next step endlessly hanging instead of failing fast. This is bad because when arcasHLA is being used within a larger pipeline, that larger pipeline is stuck waiting for a process that will never finish, instead of becoming aware there was an error.

From the tail end of the stderr of the hanging process:

        samtools view -@8 -f 2 /wrk/-263446968/SF-066.Aligned.sortedByCoord.out.bam chr6 >> /tmp/arcas_275536da-9e6d-4318-b819-fbb7c3a4c26a/SF-066.Aligned.sortedByCoord.out.hla.sam

        samtools view: writing to standard output failed: No space left on device
        samtools view: error closing standard output: -1

[extract] Converting SAM to BAM: 

        samtools view -Sb -@8 /tmp/arcas_275536da-9e6d-4318-b819-fbb7c3a4c26a/SF-066.Aligned.sortedByCoord.out.hla.sam > /tmp/arcas_275536da-9e6d-4318-b819-fbb7c3a4c26a/SF-066.Aligned.sortedByCoord.out.hla.bam