tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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ERROR: - can not rea' sequence #2 of 1 files #289

Closed spencer411 closed 2 years ago

spencer411 commented 2 years ago

Straight from terminal with "cat sample.tab" afterward. Any idea what is happening here? the three columns are definitely separated by tabs:

(base) -bash-4.2$ cat nullarbor.slurm.uagc21-01.3750434.out [14:21:37] Hello sb939359 [14:21:37] This is nullarbor.pl 2.0.20191013 [14:21:37] Send complaints to Torsten Seemann [14:21:37] Scanning --ref for problematic sequence IDs... [14:21:37] Using reference genome: /network/rit/lab/andamlab/Dowd/Ecoli/nullarbor_ecoli/NC_000913.3.fna [14:21:37] ERROR: Isolate 'PNUSAE003912-NH-M03985-170412_S13_L001' - can not rea' sequence #2 of 1 files: 'PNUSAE003912-NH-M03985-170412_S13_L001_R2.fq (base) -bash-4.2$ cat samples.tab PNUSAE003912-NH-M03985-170412_S13_L001 PNUSAE003912-NH-M03985-170412_S13_L001_R1.fq PNUSAE003912-NH-M03985-170412_S13_L001_R2.fq PNUSAE005534 PNUSAE005534_R1.fq PNUSAE005534_R2.fq PNUSAE005535 PNUSAE005535_R1.fq PNUSAE005535_R2.fq PNUSAE006112 PNUSAE006112_R1.fq PNUSAE006112_R2.fq PNUSAE006113 PNUSAE006113_R1.fq PNUSAE006113_R2.fq PNUSAE006114 PNUSAE006114_R1.fq PNUSAE006114_R2.fq PNUSAE006258 PNUSAE006258_R1.fq PNUSAE006258_R2.fq PNUSAE006259-NH-M03985-170313_S2_L001 PNUSAE006259-NH-M03985-170313_S2_L001_R1.fq PNUSAE006259-NH-M03985-170313_S2_L001_R2.fq PNUSAE006260 PNUSAE006260_R1.fq PNUSAE006260_R2.fq PNUSAE006261 PNUSAE006261_R1.fq PNUSAE006261_R2.fq PNUSAE006662 PNUSAE006662_R1.fq PNUSAE006662_R2.fq PNUSAE006663 PNUSAE006663_R1.fq PNUSAE006663_R2.fq PNUSAE006664 PNUSAE006664_R1.fq PNUSAE006664_R2.fq PNUSAE006665 PNUSAE006665_R1.fq PNUSAE006665_R2.fq PNUSAE007332 PNUSAE007332_R1.fq PNUSAE007332_R2.fq PNUSAE007333 PNUSAE007333_R1.fq PNUSAE007333_R2.fq PNUSAE007334 PNUSAE007334_R1.fq PNUSAE007334_R2.fq PNUSAE007335 PNUSAE007335_R1.fq PNUSAE007335_R2.fq PNUSAE007336 PNUSAE007336_R1.fq PNUSAE007336_R2.fq PNUSAE007337 PNUSAE007337_R1.fq PNUSAE007337_R2.fq PNUSAE007338 PNUSAE007338_R1.fq PNUSAE007338_R2.fq PNUSAE007339 PNUSAE007339_R1.fq PNUSAE007339_R2.fq PNUSAE007340 PNUSAE007340_R1.fq PNUSAE007340_R2.fq PNUSAE008395 PNUSAE008395_R1.fq PNUSAE008395_R2.fq PNUSAE008396 PNUSAE008396_R1.fq PNUSAE008396_R2.fq PNUSAE008397 PNUSAE008397_R1.fq PNUSAE008397_R2.fq PNUSAE009260 PNUSAE009260_R1.fq PNUSAE009260_R2.fq PNUSAE009262 PNUSAE009262_R1.fq PNUSAE009262_R2.fq PNUSAE009263 PNUSAE009263_R1.fq PNUSAE009263_R2.fq PNUSAE009264 PNUSAE009264_R1.fq PNUSAE009264_R2.fq PNUSAE009266-NH-M03985-170829_S21_L001 PNUSAE009266-NH-M03985-170829_S21_L001_R1.fq PNUSAE009266-NH-M03985-170829_S21_L001_R2.fq PNUSAE009784 PNUSAE009784_R1.fq PNUSAE009784_R2.fq PNUSAE009785-NH-M03985-170914_S16_L001 PNUSAE009785-NH-M03985-170914_S16_L001_R1.fq PNUSAE009785-NH-M03985-170914_S16_L001_R2.fq PNUSAE010076 PNUSAE010076_R1.fq PNUSAE010076_R2.fq PNUSAE010077 PNUSAE010077_R1.fq PNUSAE010077_R2.fq PNUSAE010581-NH-M03985-171027_S12_L001 PNUSAE010581-NH-M03985-171027_S12_L001_R1.fq PNUSAE010581-NH-M03985-171027_S12_L001_R2.fq PNUSAE010582 PNUSAE010582_R1.fq PNUSAE010582_R2.fq PNUSAE010583 PNUSAE010583_R1.fq PNUSAE010583_R2.fq PNUSAE011203 PNUSAE011203_R1.fq PNUSAE011203_R2.fq PNUSAE011204 PNUSAE011204_R1.fq PNUSAE011204_R2.fq PNUSAE011205 PNUSAE011205_R1.fq PNUSAE011205_R2.fq

spencer411 commented 2 years ago

it was an issue with saving the tab file on mac, it has been fixed.