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czc / nb_distribution

novoBreak: local assembly for breakpoint detection in cancer genomes
MIT License
26 stars 6 forks source link

cant find bwa index #8

Closed QinZhen1995 closed 5 years ago

QinZhen1995 commented 5 years ago

HI !
I pretty sure I made a reference by BWA , and its directory is same as my reference fasta file , and the only different between index name with my reference name is its postfix,which one is .fa another is bwt and amb.... I also pretty sure my environment is very very right ,I can type SSMAKE and type enter get right content And i install this through git clone 2 days ago , mybe it can prove it is not version problem

THANKS for you job but its really hard for me to deal with this bug 

x??
QinZhen1995 commented 5 years ago

log erroor ` `` [E::bwa_idx_load] fail to locate the index files``` my command line

#!/bin/bash
echo "["`date +%Y-%m-%d,%H:%M:%S`"] Start novobreak"
nohup run_novoBreak.sh /data/user/XXX/software/nb_distribution/ \
    ~/XXX/XXX.fa \
    ~/XXXanaliysi/finalbams/XXXX.bam \
    ~/XXXanaliysi/finalbams/XXXX.bam 25 
echo "["`date +%Y-%m-%d,%H:%M:%S`"] finish "
ShixiangWang commented 5 years ago

You need set the directory for novoBreak as working directory.

Add the following code before you run novobreak.

cd `which run_novoBreak.sh`
QinZhen1995 commented 5 years ago

You need set the directory for novoBreak as working directory.

Add the following code before you run novobreak.

cd `which run_novoBreak.sh`

Thanks But it seems not work,First you can't cd a file,and then by reading source I notice the para only need the prefix of the fasta file . I think i found the reason of this problem ,and i hope a more specifically manual of this software will be push .