Error can not read sequence

[akarkaba]

Hi Torsten,
Recently I have sequenced 95 S.a aureus isolates using the NextSeq. I have concatenated the 4 reads using the attached command tab. For example Isolate 3
cat WA3-r69_S13_L001_R1_001.fastq.gz WA3-r69_S13_L002_R1_001.fastq.gz WA3-r69_S13_L003_R1_001.fastq.gz WA3-r69_S13_L004_R1_001.fastq.gz> WA3_R1.fastq.gz

This was done for all the isolates

When I tried to run the Nullarbor pipeline using the following code:
$nullarbor.pl --name PROJNAME --mlst saureus --ref NCTC8325_aureus_ref.gbk --input SAU.tab --outdir OUTDIR --fullanno --run

Error message
Error files.docx
Isolate 'WA12' can not read sequence #2 of 1 file
, I decreased the number of isolates to just 4 to check if the pipeline will run, and no report was generated

I decreased the number of concatenated reads to 3 per isolate, the first 10 isolates had a nice report with good depth, but still the same error for isolates 12 till 95, error in reading the sequence

The file was converted using dos2unix SAU.tab

If any feedback on this would be much appreciated
Kind Regards
Ali