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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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ERROR: Isolate 'PNUSAE003912-NH-M03985-170412_S13_L001' - can not read sequence #1 of 1 files: 'PNUSAE003912-NH-M03985-170412_S13_L001_R1.fq' #290

Closed naikd0 closed 2 years ago

naikd0 commented 2 years ago

I am running nullarbor and this error came up

[10:34:46] Hello dn927558 [10:34:46] This is nullarbor.pl 2.0.20191013 [10:34:46] Send complaints to Torsten Seemann [10:34:46] Scanning --ref for problematic sequence IDs... [10:34:46] Using reference genome: /network/rit/lab/andamlab/Dowd/Ecoli/nullarbor_ecoli/NC_000913.3.fna [10:34:46] ERROR: Isolate 'PNUSAE003912-NH-M03985-170412_S13_L001' - can not read sequence #1 of 1 files: 'PNUSAE003912-NH-M03985-170412_S13_L001_R1.fq'

The problem is I already deleted the Isolate and it is still giving me the same error. So clearly I am missing something but I cannot see it. Any help would be greatly appreciated. Thank you.

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