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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Can not read the 2nd files #273

Closed buihoangphuc412 closed 4 years ago

buihoangphuc412 commented 4 years ago

I ran the nullabor by this code nullarbor.pl --name Helicobacter --mlst Helicobacter_pylori --ref Comparative\ assembly/26695.fasta --input Strains.tab --outdir Nullabor/Output But they informed me that the 2nd read files can not be read [01:19:34] Hello manager [01:19:34] This is nullarbor.pl 2.0.20191007 [01:19:34] Send complaints to Torsten Seemann [01:19:34] Scanning --ref for problematic sequence IDs... [01:19:34] Using reference genome: /media/sf_Biolinux/Comparative assembly/26695.fasta '01:19:34] ERROR: Isolate 'CKIN59' - can not read sequence #2 of 1 files: '/media/sf_Biolinux/Nullabor/Paired/C-KIN59_S11_L001_R2_001.fastq.gz I checked carefully the tab files is correct, so I attached. Could you Strains.txt

tseemann commented 4 years ago

Your input file is not in Unix text format. It seems to have been created in Windows/DOS fromat.

RUn "dfos2unix" on it.

Or remove the ^M / \r line endings