I noticed bcbio would get stuck indefinitely at this step. Last time I let it run for 1000 minutes before deciding to terminate it.
The fastqs are only about 500MB in size. The grabix files it creates always stay at about 1KB in size.
I'm using this with NextSeq 500 data generated from bcl2fastq v2.19
Also I noticed with HiSeq 3000 data it complains the reads use the solexa quality format. After that it gets stuck on the same grabix indexing step.
2 answers
bcbio-nextgen has a Google User's group: https://groups.google.com/forum/#!forum/biovalidation I'm not sure of the potential issue off hand but that may be a better place to get help quickly. The devs and other users tend to be pretty active on there.
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