Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error:
[mem_sam_pe] paired reads have different names: "HWI-D00360:5:H814YADXX:1:2111:20284:33068", "HWI-D00360:5:H814YADXX:1:1213:17580:34847"
bwa mem -M ref.fa "<(cat U0a_CGATGT_L001_R1_004.fastq U0a_CGATGT_L001_R1_005.fastq U0a_CGATGT_L002_R1_001.fastq U0a_CGATGT_L002_R1_002.fastq U0a_CGATGT_L002_R1_003.fastq U0a_CGATGT_L001_R1_001.fastq U0a_CGATGT_L001_R1_002.fastq U0a_CGATGT_L002_R1_004.fastq U0a_CGATGT_L001_R1_003.fastq U0a_CGATGT_L002_R1_005.fastq)" "<(cat U0a_CGATGT_L001_R2_003.fastq U0a_CGATGT_L002_R2_005.fastq U0a_CGATGT_L001_R2_004.fastq U0a_CGATGT_L001_R2_005.fastq U0a_CGATGT_L002_R2_001.fastq U0a_CGATGT_L002_R2_002.fastq U0a_CGATGT_L001_R2_001.fastq U0a_CGATGT_L002_R2_003.fastq U0a_CGATGT_L001_R2_002.fastq U0a_CGATGT_L002_R2_004.fastq)" > out.sam
However the read (there were several) that threw this error does seem to be properly paired:
grep 'HWI-D00360:5:H814YADXX:1:2111:20284:33068' *.fastq U0a_CGATGT_L001_R1_004.fastq:@HWI-D00360:5:H814YADXX:1:2111:20284:33068 1:N:0:CGATGT U0a_CGATGT_L001_R2_004.fastq:@HWI-D00360:5:H814YADXX:1:2111:20284:33068 2:N:0:CGATGT
I can see that the concatenation of the input files is happening in a different order, so this is the next thing I'm going to try to fix, but has anyone else run into this?
(I probably just answered my own question but I'll post it anyway, that may or may not be the issue)