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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
139 stars 53 forks source link

Why is there a problem? #61

Closed yubau1112 closed 5 years ago

yubau1112 commented 5 years ago

[yubau@CNUH-i7 ~]$

python /local_work/bin/bwa-meth/bwameth.py -t 12 --reference /DataShare/Transcriptome/Homo_sapiens/NCBI/ GRCh38/Sequence/BWAIndex/version0.6.0/genome.fa.bwameth.c2t /home/yubau/Methylation/26-meth_S44_R1_001.fastq.gz /home/yubau/Methylation/26-meth_S44_R2_001.fastq.gz > /home/yubau/26-meth_S44.sam

Traceback (most recent call last): File "/local_work/bin/bwa-meth/bwameth.py", line 509, in main(sys.argv[1:]) File "/local_work/bin/bwa-meth/bwameth.py", line 506, in main set_as_failed=args.set_as_failed) File "/local_work/bin/bwa-meth/bwameth.py", line 315, in bwa_mem raise BWAMethException("first run bwameth.py index %s" % fa) main.BWAMethException: first run bwameth.py index /DataShare/Transcriptome/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/v ersion0.6.0/genome.fa.bwameth.c2t

yes i already execute "bwameth.py index $REF"

[yubau@CNUH-i7 ~]$ ls /DataShare/Transcriptome/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/ genome.fa
genome.fa.ann
genome.fa.bwameth.c2t.amb
genome.fa.bwameth.c2t.bwt
genome.fa.bwameth.c2t.sa
genome.fa.fai genome.fa.sa genome.fa.amb
genome.fa.bwameth.c2t
genome.fa.bwameth.c2t.ann
genome.fa.bwameth.c2t.pac
genome.fa.bwt
genome.fa.pac

[yubau@CNUH-i7 bwa-meth]$ ls bam-merge-pairs.py
bwameth.py
compare
example
ez_setup.py
LICENSE
paper
README.md
requirements.txt
scripts
setup.py [yubau@CNUH-i7 bwa-meth]$ pwd /local_work/bin/bwa-meth

[yubau@CNUH-i7 bwa-meth]$ python -V Python 2.7.15 :: Anaconda, Inc. [yubau@CNUH-i7 bwa-meth]$ samtools --version samtools 1.9 Using htslib 1.9 Copyright (C) 2018 Genome Research Ltd.

[yubau@CNUH-i7 bwa-meth]$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.17-r1188

Why is there a problem?

brentp commented 5 years ago

send: GRCh38/Sequence/BWAIndex/version0.6.0/genome.fa as the reference, not: GRCh38/Sequence/BWAIndex/version0.6.0/genome.fa.bwameth.c2t