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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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Exception("bad or empty fastqs") #91

Open kea027 opened 8 months ago

kea027 commented 8 months ago

I have confirmed my fastq files are accurate but bwa-meth is pulling the raise Exception("bad or empty fastqs"). It seems to pull this exception right at the end of the alignment. Is there a method to fix this error?

brentp commented 8 months ago

it seems that you have no alignments. Can you show the first few and last few lines of your fastqs and the full stderr of the bwameth run?

kea027 commented 8 months ago

stderr: M::mem_process_seqs] Processed 1649302 reads in 1529.820 CPU sec, 848.893 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -T 40 -B 2 -L 10 -CM -U 100 -p -R @RG\tID:RVF_36hr_S4_R_001val\tSM:RVF_36hr_S4_R_001val -t 30 -o /PATH/RVF_36hr_S4_methylome_new.bam References/Chlorocebus_sabaeus.ChlSab1.1.dnal.fa.bwameth.c2t /dev/stdin [main] Real time: 51218.648 sec; CPU: 92491.098 sec Traceback (most recent call last): File "/home/user/anaconda3/envs/methylation/bin/bwameth.py", line 563, in main(sys.argv[1:]) File "/home/user/anaconda3/envs/methylation/bin/bwameth.py", line 559, in main do_not_penalize_chimeras=args.do_not_penalize_chimeras) File "/home/user/anaconda3/envs/methylation/bin/bwameth.py", line 370, in bwa_mem as_bam(cmd, fa, set_as_failed, do_not_penalize_chimeras) File "/home/user/anaconda3/envs/methylation/bin/bwameth.py", line 387, in as_bam raise Exception("bad or empty fastqs") Exception: bad or empty fastqs

Fastq files head/tails R1: head @VL00388:12:AACT2TTM5:1:1101:18421:1000 1:N:0:CCAGTATC+ATCTCGCT GTTGTATAAATATTTATTATAGTTTTTATTTTTAATTTTTTTGGGTAAATATTTAGAAGTAGAAGTATTAGATTATATAGTAATTTTGTTTAATTTTTTGAAGAATTTTTTATTATATTATTATTTATGTTAGTTTATATTTTTATTAGT + CCCCCCCCC;C-CCC;CCCCCCCCCCCCCCC-CC-CCCCCCCCCCCC--CCCCCCCC-;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCC-CCCCCC-;C;CCCCCCCCCCCCC @VL00388:12:AACT2TTM5:1:1101:18875:1000 1:N:0:CCAGTATC+ATCTCGCT GGTCGGGAGGACGTTTTTGGTTCGGCGTTGTTTCGGCGTGTGTTTTGGGGTCGATTAGAGGGTTTTGGGTGTTTTGTGTTTGGTTGCGATGGTGGTGATTTTGGGGATAGATGTTCGTGTCGCGGGTTTTTTGGGTCGGCGGCGTGGTC + C;C;CCCCCCCCC-CCCCCCCCC;CCCCCCCCCCCCCCCCCCC-CCCCCCCCC--CC;-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCCCCCCC-CCCCCCC;CCCCCCCCC;CCCCCCCCCCCCCCCC-CCCCCC @VL00388:12:AACT2TTM5:1:1101:19027:1000 1:N:0:CCAGTATC+ATCTCGCT TTATTGAAAAGGTGAATAAATATTTTATTATTTTTTGTTAGTGTTATATGAAAATTTTGTTTAAAAGAGAAAATTAAATTGTATTTTTTTTTAGTGTATTATTAATATTAAAGTTAATTTAATAAAATATTATAAATAAATTTCTTTAATT

R1 tail: + CCCCCC;CCCCCCCCCCCCCCCCCCCCCCCC;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCC-;--C-C;C-C-CCCCCC;;CC;CCC-CC-CCCC--C-CCC-CCCC-C--C;CC--C-CCCCC-CCC-CCCC;C @VL00388:12:AACT2TTM5:1:2611:65267:56394 1:N:0:CCAGTATC+ATCTCGCT GAGGTGTTTAATTTGGTTATGTAGAATGTAGTTGGGTTGTTTGAAATGAAATAAAGTGGTTATTTTGAAGGAGGTGTTGTTTTTGGGTTGGTTTAGGTTGAGTTAGAGTAGATGTTATTTTTATGTTA + CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCC;CCCCCCCCCCCCCCCCCC;;-CCCCCCCCCCCCCCCCCCC-CCCCCCCCCCC;CCCCCCCCCCCCCCCCCCC;CCCC-CCCCCCCCCC @VL00388:12:AACT2TTM5:1:2611:65381:56394 1:N:0:CCAGTATC+ATCTCGCT TTAGTTTTTTTATAGTTATTAGTGAATGTTTTGTTTGATGTTTTTAGATGTTAGTTTGGGTGTAGGTTGGTTTTGGGAGTTAGTTTTAGAGTTTGTTATTTAAGTTTATTTAATTTGTTGATATGTTTGTTTTTGGAGTTTTTATTTTT + C;CCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCC;CCCCCCCCCCCCCC;-CC-CCCC-C--C;CC;;CCC-CCCCCC;CCCCC--CCC-CCCCCCCCCCCCCC;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

R2 head: @VL00388:12:AACT2TTM5:1:1101:18421:1000 2:N:0:CCAGTATC+ATCTCGCT CATCAAAAACCATTTAACACATTACTTAAATCAATTAAAACCTTTATATACTACTAATAAAAATATAAACTAACATAAATAATAATATNATAAAAAATTCTTCAAAAAATTAAACAAAATTACTATATAATCTAAATCTTCTACTTCTA + CCCCCCCCC-CCCCCCCCCCC;CCC;CCC-CC-CCCCCC-CCCCC-C;CC;CCCCCCC-;CC-CCC;;-C---C--;CCCC-CCC;CC#CCC;---CCCCCCC-;;CC-;C;C-CCCC;-CCC;;C-;-;CC-C;--;C-C;-CCCCCC @VL00388:12:AACT2TTM5:1:1101:18875:1000 2:N:0:CCAGTATC+ATCTCGCT TCTCCAACGACAAGTCGCCAAAAAACAACGTATCAACAATAACCCGATAACCCAAAATACCGACTCGAAATAAAAAATATTCCTCCCCNAAAAACAAAAAATCGAACCTCCGACCACGCCGCCGACCCAAAAAACCCGCGACTCGAACATC + CCCCCC;;C-CCCCCCCCCCCC;CCCCCCCC;CC;C;--C-CCCCCC;C-C;CC;-C;-CCCC;CCCCCCC--CC-;CCC;-CC;CC-#;-C;-CC;C;-;CCCCCCC-;;CCCC-CCC;C--CC-;--C-CC--C-;C;CC-C;---C-C @VL00388:12:AACT2TTM5:1:1101:19027:1000 2:N:0:CCAGTATC+ATCTCGCT TTAAATTAAAAAAATAAAAAAAAATAACAAAAAAAACTAAATAAATATAAAAAATTACAAAAAAAAAAAAAATTAAAAAAATTTTTAANAATTTTTTCGTATTGTTATAATTCTTTTGTATTATATCATCTATTTTTATTTTAATAT

R2 tail: + CCC;CCCCCCCCCC;-CCCCCCCCCCCCCCCCCCCCCCCC;CCCCCCCC-CCC;C;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;C-CCCCCC;CCCCCCCCCCCCCCCCCC;CCCCCCCCCCCCC;--CCCC--CCCC--C-- @VL00388:12:AACT2TTM5:1:2611:65267:56394 2:N:0:CCAGTATC+ATCTCGCT TTAACATAAAAATAACATCTACTCTAACTCAACCTAAACCAACCCAAAAACAACACCTCCTTCAAAATAACCACTTTATTTCATTTCAAACAACCCAACTACATTCTACATAACCAAATTAAACACCTC + CCCCCCCCCCCCC-CCCCCCCCCCC-;CCCCCCCCCC-CCCCCCCC;CC;CCC;---CCC;CCCC;CCCCCC;;CCCCC;CC-CCCCC-CC;C;CCC;CC-CC;CCCCCCC-CCCCC;CC;CCC-;CCC @VL00388:12:AACT2TTM5:1:2611:65381:56394 2:N:0:CCAGTATC+ATCTCGCT TACCCACGATACGTATATCAACAAAATATTTAACGAAAATAACAACCAAACGAATCAAAATCTCTTCATAACCTACAAAAATAAAAATTAAAACGTATTTACTAAAAATAAAAACTCCAAAAACAAACATATCAACAAATTAAATAACAT + CCCCCCCCCCCCCCCC-CCC-;-CC;CC;CC;CCCCCCCCCC-CCCCCC-CCC;CC;C-;CCCCCCCCCCCCCCCCC-CCCC-CCCCC-CCCCCC-CC--C;CCCCC;CCCC;-CCCC-CCCCC-C-;----C--C-C;CCCCC;--C-C