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60鱼币
本帖最后由 wtfitis 于 2021-9-24 22:10 编辑
这是calcmem.sh
这是bbrename.sh
- #!/bin/bash
- usage(){
- echo "
- Written by Brian Bushnell
- Last modified April 1, 2020
- Description: Renames reads to <prefix>_<number> where you specify the prefix
- and the numbers are ordered. There are other renaming modes too.
- If reads are paired, pairs should be processed together; if reads are
- interleaved, the interleaved flag should be set. This ensures that if a
- read number (such as 1: or 2:) is added, it will be added correctly.
- Usage: rename.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> prefix=<>
- in2 and out2 are for paired reads and are optional.
- If input is paired and there is only one output file, it will be written interleaved.
- Parameters:
- prefix= The string to prepend to existing read names.
- ow=f (overwrite) Overwrites files that already exist.
- zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
- int=f (interleaved) Determines whether INPUT file is considered interleaved.
- fastawrap=70 Length of lines in fasta output.
- minscaf=1 Ignore fasta reads shorter than this.
- qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
- qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
- ignorebadquality=f (ibq) Fix out-of-range quality values instead of crashing with a warning.
- Renaming modes (if not default):
- renamebyinsert=f Rename the read to indicate its correct insert size.
- renamebymapping=f Rename the read to indicate its correct mapping coordinates.
- renamebytrim=f Rename the read to indicate its correct post-trimming length.
- addprefix=f Rename the read by prepending the prefix to the existing name.
- prefixonly=f Only use the prefix; don't add _<number>
- addunderscore=t Add an underscore after the prefix (if there is a prefix).
- addpairnum=t Add a pairnum (e.g. ' 1:') to paired reads in some modes.
- fixsra=f Fixes headers of SRA reads renamed from Illumina.
- Specifically, it converts something like this:
- SRR17611.11 HWI-ST79:17:D091UACXX:4:1101:210:824 length=75
- ...into this:
- HWI-ST79:17:D091UACXX:4:1101:210:824 1:
- Sampling parameters:
- reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
- Java Parameters:
- -Xmx This will set Java's memory usage, overriding autodetection.
- -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
- The max is typically 85% of physical memory.
- -eoom This flag will cause the process to exit if an
- out-of-memory exception occurs. Requires Java 8u92+.
- -da Disable assertions.
- Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
- "
- }
- #This block allows symlinked shellscripts to correctly set classpath.
- 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="-Xmx1g"
- set=0
- if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
- usage
- exit
- fi
- calcXmx () {
- source "$DIR""/calcmem.sh"
- setEnvironment
- parseXmx "$@"
- }
- calcXmx "$@"
- function rename() {
- local CMD="java $EA $EOOM $z $CP -cp jgi.RenameReads $@"
- echo $CMD >&2
- eval $CMD
- }
- rename "$@"
复制代码
我程序运行bbrename.sh就出错了。。Error: Could not find or load main class jgi.RenameReads
这个class在那个文件夹下面是有的,但是为什么就是无法载入。。不太懂java
这是在centos下运行的。。
这个是运行命令- java -ea -Xmx1g -classpath /02.antisense/BBMap-master/sh/current/ jgi.RenameReads
复制代码
02.antisense/BBMap-master/current/jgi/RenameReads.java
这个文件的确存在 没办法载入
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