Comments (2)
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?
from bwa-meth.
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_001_val_\tSM:RVF_36hr_S4_R_001_val_ -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
from bwa-meth.
Related Issues (20)
- Output of bwa-meth in BAM format HOT 1
- The link in `README.md` of the `compare/` folder is not working HOT 4
- [Release Request] make a release since bwa-mem2 index are not included in current version HOT 1
- bwa-meth index error HOT 12
- bwa-mem2 cannot recognize the input from the pipe HOT 5
- broken pipeline HOT 3
- `handle_header` mangles alt contigs HOT 2
- Unique mapped reads HOT 1
- Q: Issues with installation 0.2.5 HOT 1
- Timestamp checking of .fa files prevents me from running bwa-meth in the cloud HOT 2
- Meet Error When running bwa meth mem2
- Help command for aligner command does not work HOT 1
- unrecognized reference name during sam_parse HOT 9
- repeated alignment (bwa get stuck) HOT 2
- when running bwameth example, exception: AttributeError: module 'toolshed.files' has no attribute 'prefunc' HOT 2
- BWA-meth mapping issues
- Overriding hardcoded -B values is possible from command line HOT 3
- YC and MD tag issue HOT 3
- YC and YD tags HOT 1
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from bwa-meth.