Closed spencer411 closed 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
it was an issue with saving the tab file on mac, it has been fixed.
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