[已解决]Error: Could not find or load main class jgi.RenameReads

wtfitis

这是calcmem.sh

1. #!/bin/bash
   
2. 
   
3. #usage(){
   
4. #        echo "CalcMem v1.15"
   
5. #        echo "Written by Brian Bushnell, Doug Jacobsen, Alex Copeland, Bryce Foster"
   
6. #        echo "Calculates available memory in megabytes"
   
7. #        echo "Last modified December 17, 2019"
   
8. #}
   
9. 
   
10. #Also parses other Java flags
    
11. function parseXmx () {
    
12.        
    
13.         local setxmx=0
    
14.         local setxms=0
    
15.        
    
16.         for arg in "$@"
    
17.         do
    
18.                 if [[ "$arg" == "Xmx="* ]] || [[ "$arg" == "xmx="* ]]; then
    
19.                         z="-Xmx"${arg:4}
    
20.                         setxmx=1
    
21.                 elif [[ "$arg" == "-Xmx="* ]] || [[ "$arg" == "-xmx="* ]]; then
    
22.                         z="-Xmx"${arg:5}
    
23.                         setxmx=1
    
24.                 elif [[ "$arg" == -Xmx* ]] || [[ "$arg" == -xmx* ]]; then
    
25.                         #z="$arg"
    
26.                         z="-X"${arg:2}
    
27.                         setxmx=1
    
28.                 elif [[ "$arg" == Xmx* ]] || [[ "$arg" == xmx* ]]; then
    
29.                         #z="-$arg"
    
30.                         z="-X"${arg:1}
    
31.                         setxmx=1
    
32.                 elif [[ "$arg" == -Xms* ]]; then
    
33.                         z2="$arg"
    
34.                         setxms=1
    
35.                 elif [[ "$arg" == Xms* ]]; then
    
36.                         z2="-$arg"
    
37.                         setxms=1
    
38.                 elif [[ "$arg" == -da ]] || [[ "$arg" == -ea ]]; then
    
39.                         EA="$arg"
    
40.                 elif [[ "$arg" == da ]] || [[ "$arg" == ea ]]; then
    
41.                         EA="-$arg"
    
42.                 elif [[ "$arg" == ExitOnOutOfMemoryError ]] || [[ "$arg" == exitonoutofmemoryerror ]] || [[ "$arg" == eoom ]]; then
    
43.                         EOOM="-XX:+ExitOnOutOfMemoryError"
    
44.                 elif [[ "$arg" == -ExitOnOutOfMemoryError ]] || [[ "$arg" == -exitonoutofmemoryerror ]] || [[ "$arg" == -eoom ]]; then
    
45.                         EOOM="-XX:+ExitOnOutOfMemoryError"
    
46.                 elif [[ "$arg" == json ]] || [[ "$arg" == "json=t" ]] || [[ "$arg" == "json=true" ]] || [[ "$arg" == "format=json" ]]; then
    
47.                         json=1
    
48.                 elif [[ "$arg" == silent ]] || [[ "$arg" == "silent=t" ]] || [[ "$arg" == "silent=true" ]]; then
    
49.                         silent=1
    
50.                 fi
    
51.         done
    
52.        
    
53.         if [[ $setxmx == 1 ]] && [[ $setxms == 0 ]]; then
    
54.                 local substring=`echo $z| cut -d'x' -f 2`
    
55.                 z2="-Xms$substring"
    
56.                 setxms=1
    
57.         elif [[ $setxmx == 0 ]] && [[ $setxms == 1 ]]; then
    
58.                 local substring=`echo $z2| cut -d's' -f 2`
    
59.                 z="-Xmx$substring"
    
60.                 setxmx=1
    
61.         fi
    
62.        
    
63.         set=$setxmx
    
64.        
    
65. }
    
66. 
    
67. function setEnvironment(){
    
68. 
    
69.         EA="-ea"
    
70.         EOOM=""
    
71. 
    
72.         if [[ $SHIFTER_RUNTIME == 1 ]]; then
    
73.                 #Ignore NERSC_HOST
    
74.                 shifter=1
    
75.         elif [ -v "$EC2_HOME" ]; then
    
76.                 #Let's assume this is the AWS taxonomy server...
    
77.                 PATH=/test1/binaries/bgzip:$PATH
    
78.                 PATH=/test1/binaries/lbzip2/bin:$PATH
    
79.                 PATH=/test1/binaries/sambamba:$PATH
    
80.                 #PATH=/test1/binaries/java/jdk-11.0.2/bin:$PATH
    
81.                 PATH=/test1/binaries/pigz2/pigz-2.4:$PATH
    
82.         elif [ -z "$NERSC_HOST" ]; then
    
83.                 #Not NERSC; do nothing
    
84.                 :
    
85.         else
    
86.                 PATH=/global/projectb/sandbox/gaag/bbtools/bgzip:$PATH
    
87.                 PATH=/global/projectb/sandbox/gaag/bbtools/lbzip2/bin:$PATH
    
88.                 PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH
    
89.                 PATH=/global/projectb/sandbox/gaag/bbtools/java/jdk-11.0.2/bin:$PATH
    
90.                 PATH=/global/projectb/sandbox/gaag/bbtools/pigz2/pigz-2.4:$PATH
    
91.                
    
92.                 if [[ $NERSC_HOST == cori ]]; then
    
93. 
    
94.                         #module unload PrgEnv-intel
    
95.                         #module load PrgEnv-gnu/7.1
    
96.                         PATH=/global/projectb/sandbox/gaag/bbtools/samtools_cori/bin:$PATH
    
97.                         :
    
98.                 fi
    
99.         fi
    
100. }
     
101. 
     
102. function freeRam(){
     
103.         RAM=0;
     
104. 
     
105.         #Memory is in kilobytes.
     
106.         local defaultMem=3200000
     
107.         if [ $# -gt 0 ]; then
     
108.                 defaultMem=$1;
     
109.                 case $defaultMem in
     
110.                         *g)
     
111.                         defaultMem=`echo $defaultMem| cut -d'g' -f 1`
     
112.                         defaultMem=$(( $defaultMem * $(( 1024 * 1024 )) ))
     
113.                         ;;
     
114.                         *m)
     
115.                         defaultMem=`echo $defaultMem| cut -d'm' -f 1`
     
116.                         defaultMem=$(( $defaultMem * 1024 ))
     
117.                         ;;
     
118.                         *k)
     
119.                         defaultMem=`echo $defaultMem| cut -d'k' -f 1`
     
120.                         ;;
     
121.                 esac
     
122.         fi
     
123. 
     
124.         local mult=84
     
125.         if [ $# -gt 1 ]; then
     
126.                 mult=$2;
     
127.         fi
     
128.        
     
129.         #echo "mult =    $mult" # percent of memory to allocate
     
130.         #echo "default = $defaultMem"
     
131.        
     
132.         local ulimit=$(ulimit -v)
     
133.         ulimit="${ulimit:-0}"
     
134.         if [ "$ulimit" = "unlimited" ]; then ulimit=0; fi
     
135.         local x=$ulimit
     
136.         #echo "x = ${x}" # normally ulimit -v
     
137.        
     
138.         #local HOSTNAME=`hostname`
     
139.         local sge_x=0
     
140.         local slurm_x=$(( SLURM_MEM_PER_NODE * 1024 ))
     
141. 
     
142.         if [[ $RQCMEM -gt 0 ]]; then
     
143.                 #echo "branch for manual memory"
     
144.                 x=$(( RQCMEM * 1024 ));
     
145.         elif [ -e /proc/meminfo ]; then
     
146.                 local vfree=$(cat /proc/meminfo | awk -F: 'BEGIN{total=-1;used=-1} /^CommitLimit:/ { total=$2 }; /^Committed_AS:/ { used=$2 } END{ print (total-used) }')
     
147.                 local pfree=$(cat /proc/meminfo | awk -F: 'BEGIN{free=-1;cached=-1;buffers=-1} /^MemFree:/ { free=$2 }; /^Cached:/ { cached=$2}; /^Buffers:/ { buffers=$2} END{ print (free+cached+buffers) }')
     
148.                
     
149.                 #echo "vfree =   $vfree"
     
150.                 #echo "pfree =   $pfree"
     
151.                 #echo "ulimit =  $ulimit"
     
152. 
     
153.                 local x2=0;
     
154. 
     
155.                
     
156.                 if [ $vfree -gt 0 ] && [ $pfree -gt 0 ]; then
     
157.                         if [ $vfree -gt $pfree ]; then x2=$pfree;
     
158.                         else x2=$vfree; fi
     
159.                 elif [ $vfree -gt 0 ]; then x2=$vfree;
     
160.                 elif [ $pfree -gt 0 ]; then x2=$pfree;
     
161.                 fi
     
162. 
     
163.                 #echo $sge_x
     
164.                 #echo $slurm_x
     
165.                 #echo $x
     
166.                 #echo $x2
     
167. 
     
168.                 # set to SGE_HGR_RAMC or SLURM_MEM_PER_NODE value
     
169.                 if [ $sge_x -gt 0 ]; then
     
170.                         if [ $x2 -gt $sge_x ] || [ $x2 -eq 0 ]; then
     
171.                                 x=$sge_x;
     
172.                                 x2=$x;
     
173.                         fi
     
174.                 elif [ $slurm_x -gt 0 ]; then
     
175.                         if [ $x2 -gt $slurm_x ] || [ $x2 -eq 0 ]; then
     
176.                                 x=$slurm_x;
     
177.                                 x2=$x;
     
178.                         fi
     
179.                 fi
     
180.                
     
181.                 #echo "x = ${x}"
     
182.                 #echo "x2 = ${x2}"
     
183.                 #echo $vfree
     
184.                 #echo $pfree
     
185.                
     
186.                 if [ "$x" = "unlimited" ] || (("$x" > $x2)); then x=$x2; fi
     
187.                 if [ $x -lt 1 ]; then x=$x2; fi
     
188.         fi
     
189. 
     
190.         if [ $x -lt 1 ] || [[ $HOSTNAME == genepool* ]]; then
     
191.                 #echo "branch for unknown memory"
     
192.                 #echo $x
     
193.                 #echo "ram is unlimited"
     
194.                 RAM=$((defaultMem/1024))
     
195.                 echo "Max memory cannot be determined.  Attempting to use $RAM MB." 1>&2
     
196.                 echo "If this fails, please add the -Xmx flag (e.g. -Xmx24g) to your command, " 1>&2
     
197.                 echo "or run this program qsubbed or from a qlogin session on Genepool, or set ulimit to an appropriate value." 1>&2
     
198.         else
     
199.                 #echo "branch for known memory"
     
200.                 #echo "x = ${x}"
     
201.                 #echo "m = ${mult}"
     
202.                
     
203.                 # available (ram - 500k) * 85% / 1024kb = megs of ram to use
     
204.                 # not sure where this formula came from
     
205.                 RAM=$(( ((x-500000)*mult/100)/1024 ))
     
206.                 #echo $RAM
     
207.         fi
     
208.         #local z="-Xmx${RAM}m"
     
209.         #echo $RAM
     
210.         return 0
     
211. }
     
212. 
     
213. #freeRam "$@"

复制代码

这是bbrename.sh

1. #!/bin/bash
   
2. 
   
3. usage(){
   
4. echo "
   
5. Written by Brian Bushnell
   
6. Last modified April 1, 2020
   
7. Description:  Renames reads to <prefix>_<number> where you specify the prefix
   
8. and the numbers are ordered.  There are other renaming modes too.
   
9. If reads are paired, pairs should be processed together; if reads are
   
10. interleaved, the interleaved flag should be set.  This ensures that if a
    
11. read number (such as 1: or 2:) is added, it will be added correctly.
    
12. Usage:  rename.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> prefix=<>
    
13. in2 and out2 are for paired reads and are optional.
    
14. If input is paired and there is only one output file, it will be written interleaved.
    
15. Parameters:
    
16. prefix=             The string to prepend to existing read names.
    
17. ow=f                (overwrite) Overwrites files that already exist.
    
18. zl=4                (ziplevel) Set compression level, 1 (low) to 9 (max).
    
19. int=f               (interleaved) Determines whether INPUT file is considered interleaved.
    
20. fastawrap=70        Length of lines in fasta output.
    
21. minscaf=1           Ignore fasta reads shorter than this.
    
22. qin=auto            ASCII offset for input quality.  May be 33 (Sanger), 64 (Illumina), or auto.
    
23. qout=auto           ASCII offset for output quality.  May be 33 (Sanger), 64 (Illumina), or auto (same as input).
    
24. ignorebadquality=f  (ibq) Fix out-of-range quality values instead of crashing with a warning.
    
25. Renaming modes (if not default):
    
26. renamebyinsert=f    Rename the read to indicate its correct insert size.
    
27. renamebymapping=f   Rename the read to indicate its correct mapping coordinates.
    
28. renamebytrim=f      Rename the read to indicate its correct post-trimming length.
    
29. addprefix=f         Rename the read by prepending the prefix to the existing name.
    
30. prefixonly=f        Only use the prefix; don't add _<number>
    
31. addunderscore=t     Add an underscore after the prefix (if there is a prefix).
    
32. addpairnum=t        Add a pairnum (e.g. ' 1:') to paired reads in some modes.
    
33. fixsra=f            Fixes headers of SRA reads renamed from Illumina.
    
34.                     Specifically, it converts something like this:
    
35.                     SRR17611.11 HWI-ST79:17:D091UACXX:4:1101:210:824 length=75
    
36.                     ...into this:
    
37.                     HWI-ST79:17:D091UACXX:4:1101:210:824 1:
    
38. Sampling parameters:
    
39. reads=-1            Set to a positive number to only process this many INPUT reads (or pairs), then quit.
    
40. Java Parameters:
    
41. -Xmx                This will set Java's memory usage, overriding autodetection.
    
42.                     -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
    
43.                     The max is typically 85% of physical memory.
    
44. -eoom               This flag will cause the process to exit if an
    
45.                     out-of-memory exception occurs.  Requires Java 8u92+.
    
46. -da                 Disable assertions.
    
47. Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
    
48. "
    
49. }
    
50. 
    
51. #This block allows symlinked shellscripts to correctly set classpath.
    
52. pushd . > /dev/null
    
53. DIR="${BASH_SOURCE[0]}"
    
54. while [ -h "$DIR" ]; do
    
55.   cd "$(dirname "$DIR")"
    
56.   DIR="$(readlink "$(basename "$DIR")")"
    
57. done
    
58. cd "$(dirname "$DIR")"
    
59. DIR="$(pwd)/"
    
60. popd > /dev/null
    
61. 
    
62. #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
    
63. CP="$DIR""current/"
    
64. 
    
65. z="-Xmx1g"
    
66. set=0
    
67. 
    
68. if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
    
69.         usage
    
70.         exit
    
71. fi
    
72. 
    
73. calcXmx () {
    
74.         source "$DIR""/calcmem.sh"
    
75.         setEnvironment
    
76.         parseXmx "$@"
    
77. }
    
78. calcXmx "$@"
    
79. 
    
80. function rename() {
    
81.         local CMD="java $EA $EOOM $z $CP -cp jgi.RenameReads $@"
    
82.         echo $CMD >&2
    
83.         eval $CMD
    
84. }
    
85. 
    
86. 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

1. 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

最佳答案

月排行榜 / 总排行榜

AdiosSpike

2021-9-24 21:22:37

谢谢

跳转到最佳答案楼层

AdiosSpike

谢谢

wtfitis

有没有帮帮我的。。头皮发麻了

AdiosSpike

幸福来得太突然当时以为是回复得鱼币的那种，我现在才接触C语言暂时没办法解决，抱歉，谢谢你的鱼币，我会好好学习的

wtfitis

AdiosSpike 发表于 2021-10-1 22:55
幸福来得太突然当时以为是回复得鱼币的那种，我现在才接触C语言暂时没办法解决，抱歉，谢谢你的 ...

我已经搞定了 嘿嘿

AdiosSpike

wtfitis 发表于 2021-10-7 09:48
我已经搞定了 嘿嘿

哈哈哈 恭喜恭喜 虽然我是初学者 但每次把bug找出来的时候确实很棒
大佬 继续加油哦