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I just spent three days debugging a 'feature' that is undocumented and unexpected: cellranger 'hunts' for samples recursively under the DIR specified by the --fastqs argument. The background to this is that I had to doctor some fastq files but keep the same name to be compatible with the rest of our infrastructure. So I did something like
cd /hpc/cache/fastq
mkdir orig
mv LX413* orig/
mv ~/tmp/subsampled/LX413* ./
just so I could use our launcher and database, yet keep the originals in cache. This behaviour is completely undocumented and what's worse, the resulting error message is misleading:
Duplicate FASTQs found between Sample LX413 in "/hpc/cache/fastq" and Sample LX413 in "/hpc/cache/fastq"
this should have been
Duplicate FASTQs found between Sample LX413 in "/hpc/cache/fastq" and Sample LX413 in "/hpc/cache/fastq/orig"
The text was updated successfully, but these errors were encountered:
I just spent three days debugging a 'feature' that is undocumented and unexpected: cellranger 'hunts' for samples recursively under the
DIR
specified by the--fastqs
argument. The background to this is that I had to doctor some fastq files but keep the same name to be compatible with the rest of our infrastructure. So I did something likejust so I could use our launcher and database, yet keep the originals in cache. This behaviour is completely undocumented and what's worse, the resulting error message is misleading:
Duplicate FASTQs found between Sample LX413 in "/hpc/cache/fastq" and Sample LX413 in "/hpc/cache/fastq"
this should have been
Duplicate FASTQs found between Sample LX413 in "/hpc/cache/fastq" and Sample LX413 in "/hpc/cache/fastq/orig"
The text was updated successfully, but these errors were encountered: