eg, input files sampleA_1-WT-V-A_1.fq.gz and sampleA_1-WT-V-A_2.fq.gz with flags -paired -pairIds _1,_2 -extn .fq.gz fails with an error:
Fatal error: /scratch/pl41/laxy/jobs/miniconda3/envs/rnasik-1.5.3/bin/../opt/rnasik-1.5.3/src/sikFqFiles.bds, line 247, pos 17. -paired set to true, but can't find _2 read. Is it single-end data? Also check your -pairIds _1,_2
Stack trace:
error "-paired set to $paired, but can't find $pai ... # /scratch/pl41/laxy/jobs/miniconda3/envs/rnasik-1.5.3/bin/../opt/rnasik-1.5.3/src/sikFqFiles.bds:247
samplesSheet = makeSamplesSheet( fqFiles,fqRgxs, ... # /scratch/pl41/laxy/jobs/miniconda3/envs/rnasik-1.5.3/bin/../opt/rnasik-1.5.3/src/RNAsik.bds:93
This is because when converting the _1 filename into the _2 filename to verify that paired files exist, string.replace is used but the substring _1 occurs twice in the first read pair.
One solution is to enforce that the pairId must be immediately before the extension, like this: pansapiens@914f029
(the side effect of this patch would be that typical Illumina instrument output eg somereads_R1_001.fastq.gz and somereads_R2_001.fastq.gz you'd probably need to specify -paired -pairIds _R1_001, R2_001 -extn .fastq.gz, or maybe -paired -pairIds _R1, R2 -extn _001.fastq.gz - untested).
eg, input files
sampleA_1-WT-V-A_1.fq.gzandsampleA_1-WT-V-A_2.fq.gzwith flags-paired -pairIds _1,_2 -extn .fq.gzfails with an error:This is because when converting the
_1filename into the_2filename to verify that paired files exist,string.replaceis used but the substring_1occurs twice in the first read pair.One solution is to enforce that the pairId must be immediately before the extension, like this: pansapiens@914f029
(the side effect of this patch would be that typical Illumina instrument output eg
somereads_R1_001.fastq.gzandsomereads_R2_001.fastq.gzyou'd probably need to specify-paired -pairIds _R1_001, R2_001 -extn .fastq.gz, or maybe-paired -pairIds _R1, R2 -extn _001.fastq.gz- untested).