I'm fairly sure this issue is be linked to Razers3, but maybe you guys have a fix for it.
My command is:
python /home/regmgbe/Programmes/OptiType/OptiTypePipeline.py -i ./C141_R1.fastq --rna -v -o ./Optitype_out
It runs until:
0:31:06.86 0 reads loaded. Creating dataframe...
The first and last lines of the error are:
[E::bam_read1] CIGAR and query sequence lengths differ for CL200152152L1C001R001_89655/1
ValueError: Length mismatch: Expected axis has 0 elements, new values have 7339 elements
Attempting to read the bam file (from the output folder) with samtools produces an identical "CIGAR and query sequence" error, so I'm guessing Razers3 has produced a faulty Bam file.
Hey!
I'm fairly sure this issue is be linked to Razers3, but maybe you guys have a fix for it.
My command is:
python /home/regmgbe/Programmes/OptiType/OptiTypePipeline.py -i ./C141_R1.fastq --rna -v -o ./Optitype_outIt runs until:
0:31:06.86 0 reads loaded. Creating dataframe...The first and last lines of the error are:
[E::bam_read1] CIGAR and query sequence lengths differ for CL200152152L1C001R001_89655/1ValueError: Length mismatch: Expected axis has 0 elements, new values have 7339 elementsAttempting to read the bam file (from the output folder) with samtools produces an identical "CIGAR and query sequence" error, so I'm guessing Razers3 has produced a faulty Bam file.