Question: Why did cellranger count fail in the CHUNK_READS stage?
Answer: Corrupt or incomplete FASTQ files are a common cause for pipeline failure in this cellranger count stage.
Corrupt or incomplete FASTQ files typically result from incomplete transfers. To verify that files are identical between source and destination, please use file checksums such as md5sum.
Below are messages in the errors and stdout files in the failed job chunk associated with this failure mode:
[errors]
...
CalledProcessError: Command '['chunk_reads', '--reads-per-fastq', '5000000', '/pipestance_id/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnkX-XXXX/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']' returned non-zero exit status 1
[stdout] ... error: fastq parsing error caused by: corrupt deflate stream running chunk reads: [['chunk_reads', '--reads-per-fastq', '5000000', '/pipestance/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnkX-XXXX/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']]