Question: What does "ERROR; return code from pthread_create() is 11" mean?
Answer: Sometimes Cell Ranger will fail with the error:
ERROR; return code from pthread_create() is 11 Error detail: Resource temporarily unavailable
The type of failure is generally not reproducible in the sense that it does not tend to occur in the same stage or job chunk.
This typically indicates that during the run you reached your system user limit for the number of "max user processes".
The recommendation in this case is to increase your user limit setting for "max user processes" (ulimit -u) or lower the number of cores used via --localcores (minimum is 8 cores) and --localmem (minimum is 64) before starting a new pipestance run.
For more information, please see the "Resource Limits" section of the Cell Ranger systems requirements page.