mapping生成sam文件时出现[mem_sam_pe] paired reads have different names错误

方法一：

用以下命令修复：

bbrename.sh in1=read1.fq in2=read2.fq out1=renamed1.fq out2=renamed2.fq 

　　bbrename.sh 下载地址网上自行搜索

对于多个fq文件，可以用以下命令：

while read line
do
      nohup bbrename.sh in=${line}_R1.fq in2=${line}_R2.fq out=${line}_R1.sh.fq out2=${line}_R2.sh.fq &     
done < name.txt #####其中，name.txt指的是包含sample名字文件

 

方法二：

 

使用repair.sh进行修复：

 

while read line
do
      nohup repair.sh in=${line}_R1.fastq in2=${line}_R2.fastq out=${line}_R1.sh.fastq out2=${line}_R2.sh.fastq &     
done < name.txt

 

repair.sh脚本：

 

 

#!/bin/bash
#repair in=<infile> out=<outfile>

usage(){
echo "
Written by Brian Bushnell
Last modified November 9, 2016

Description:  Re-pairs reads that became disordered or had some mates eliminated.

Usage:  repair.sh in=<input file> out=<pair output> outs=<singleton output>

Input may be fasta, fastq, or sam, compressed or uncompressed.


Parameters:
in=<file>       The 'in=' flag is needed if the input file is not the first 
                parameter.  'in=stdin' will pipe from standard in.
in2=<file>      Use this if 2nd read of pairs are in a different file.
out=<file>      The 'out=' flag is needed if the output file is not the second
                parameter.  'out=stdout' will pipe to standard out.
out2=<file>     Use this to write 2nd read of pairs to a different file.
outs=<file>     (outsingle) Write singleton reads here.
overwrite=t     (ow) Set to false to force the program to abort rather than
                overwrite an existing file.
showspeed=t     (ss) Set to 'f' to suppress display of processing speed.
ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
                level; lower compression is faster.
fint=f          (fixinterleaving) Fixes corrupted interleaved files using read
                names.  Only use on files with broken interleaving - correctly
                interleaved files from which some reads were removed.
repair=t        (rp) Fixes arbitrarily corrupted paired reads by using read 
                names.  Uses much more memory than 'fint' mode.
ain=f           (allowidenticalnames) When detecting pair names, allows 
                identical names, instead of requiring /1 and /2 or 1: and 2:

monitor=f       Kill this process if it crashes.  monitor=600,0.01 would kill
                after 600 seconds under 1% usage.

Java Parameters:
-Xmx            This will be passed to Java to set memory usage, overriding the program's automatic memory detection.
                -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.

Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}

pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
  cd "$(dirname "$DIR")"
  DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null

#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"

z="-Xmx4g"
z2="-Xms4g"
EA="-ea"
set=0

if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
        usage
        exit
fi

calcXmx () {
        source "$DIR""/calcmem.sh"
        parseXmx "$@"
        if [[ $set == 1 ]]; then
                return
        fi
        freeRam 4000m 84
        z="-Xmx${RAM}m"
        z2="-Xms${RAM}m"
}
calcXmx "$@"

repair() {
        if [[ $NERSC_HOST == genepool ]]; then
                module unload oracle-jdk
                module load oracle-jdk/1.8_64bit
                module load pigz
        fi
        local CMD="java $EA $z -cp $CP jgi.SplitPairsAndSingles rp $@"
        echo $CMD >&2
        eval $CMD
}

repair "$@"

 

　　　

脚本来源：https://anaconda.org/bioconda/bbmap