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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Input File Format #220

Open tetrahedraldogwood opened 6 months ago

tetrahedraldogwood commented 6 months ago

config_palmetto.txt

Hello, I keep getting the Input file error. I've gone through other's issues but can't seem to find one that matches on input (maybe I missed it though).

I attached my config file, and below are the first few lines of my input files (first line is my command, not in the file)... Forward: gzip -cd KWGF_PCRfree_NA_NA_GGACTTGG_Sabal_palmetto_I1369L1_L1_R1.trimmed.fastq.gz | head -10 @A00406:444:HW522DSX7:1:1101:1054:1000 1:N:0:GGACTTGG+CGTCTGCG TNTAGATAAACTATGATTAATTATCCTATATCAATGATTTGGTCACATCCAATTTCTTATAATTTTAGATTACCTCCTTATAAATTCCACTTGTTCAATCTTGCATTGAAATTGATCCACTAACATAAACAAATATTTAACTCAGAATTAT + F#FFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF,FFFFFF:FFFFFFF,:FFFFFF:FFFFF:FFFFFFFFFF:FF:FFF:FFF:FFFFFFFFF:FFFF:FFFFFFFFFFF:FFFFFFFFF:FFFFF:FFFF,F:FFF:FFFFF:FF @A00406:444:HW522DSX7:1:1101:1090:1000 1:N:0:GGACTTGG+CGTCTGCG TNCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTATTCTTCTTCTTCTTCTTATTCTTCTTCTTCTTCTTATTCTTCTTATTCT + :#FFFFFFF:FFFFFFF:FFFFFFFFFFF:FFFFFFFFF:FFF::,FFFF:::,F:,F:::FFFFF,:FFF,FF,F,,FF,FFFF,FF,,FF,FFFFF,::,,F,:F:F,:::,:,:,,,F:,::,:F,:,,::,:F,:F,:::,F,,F:, @A00406:444:HW522DSX7:1:1101:1253:1000 1:N:0:GGACTTGG+CGTCTGCG TNGTCTTTTTTTGTTGCACCTAATTCTTCTCCATTATAGTGCCAAGCATGGTTAAATTCTTACCTGAAAAAGAAATTTTGGATTGATCGGCTCATTTTGAGTCCCAAATGAAGTAATTTTTGCTCAATTGGTTGGGGCATGACATAGAAAA

Reverse: gzip -cd KWGF_PCRfree_NA_NA_GGACTTGG_Sabal_palmetto_I1369L1_L1_R2.trimmed.fastq.gz | head -10 @A00406:444:HW522DSX7:1:1101:1054:1000 2:N:0:GGACTTGG+CGTCTGCG GGGTTTAGAGGCAGGTTCTGTGGGCCATTTAATTTATCTAAGGCATTTTATATTTGGCTGTTGGTTAGGCTAGTAAGGTTCGAGTTAAATCAAATCGGGTTGGATTAAGTCAGAGAATCAGATTAAGTTGATTTGATCGAATCCAAGCAAA + FFFFFF,FFFF,FFFFFFFFFFFF,F,FFFFFFFFFFF::FFF:::F,F,F,F,FFFF,FF:FFFFFF:FF,FF::FFF:::FFF,F:FF:F,FF:FFF,FFFFFF,FFF:F:FFF:::FFF:FFFFF:FFFFFFFF,F:,FF:F:F,:FF @A00406:444:HW522DSX7:1:1101:1090:1000 2:N:0:GGACTTGG+CGTCTGCG AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA + ,FFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFF::FFFFFFFF:FFFFFFFFFFF:FF:FFFFFFF:FFF:FFFFFFFFFFFF:FFFFFFFFFF::F::F:F,FFF:F:,FF,F:FFFFF:FFF, @A00406:444:HW522DSX7:1:1101:1253:1000 2:N:0:GGACTTGG+CGTCTGCG GACACGATTCTCTTTTCTATGTCATGCCCCAACCAATTGAGCAAAAATTACTTCATTTGGGACTCAAAATGAGCCGATCAATCCAAAATTTCTTTTTCAGGTAAGAATTTAACCATGCTTGGCACTATAATGGAGAAGAATTAGGTGCAAC

Any help is most appreciated, thank you so much. Madi

ndierckx commented 5 months ago

Can you try version 4.3.5?