1.输入unzip命令行提示“ubuntu 环境变量失效”

Command 'unzip' is available in '/usr/bin/unzip'

The command could not be located because '/usr/bin' is not included in the PATH environment variable

解决方法:将/usr/bin写入环境变量

export PATH=/usr/bin:$PATH

最后显示

Archive:  /disk1/shares/Trimmomatic-0.38.zip

  creating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/LICENSE

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar

  creating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/NexteraPE-PE.fa

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-SE.fa

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq3-PE-2.fa

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq3-PE.fa

  inflating: /disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq3-SE.fa

成功运行

2.运行测试

java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar

Usage:

      PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <st                                                                                      atsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseo                                                                                      ut <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...

  or:

      SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <st                                                                                      atsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...

  or:

      -version

同样成功

3.原始数据过滤

mkdir trim_out

java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /disk/shares/Seqs/test_7942raw_1.fq.gz /disk/shares/Seqs/test_7942raw_2.fq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk/teaching/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75

### 把ILLUMINACLIP后的路径换为自己的，用相对路径就出错了

替换后即为：

mkdir trim_out

java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /disk/shares/Seqs/test_7942raw_1.fq.gz /disk/shares/Seqs/test_7942raw_2.fq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa

:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75

显示为

TrimmomaticPE: Started with arguments:

-phred33 /disk/shares/Seqs/test_7942raw_1.fq.gz /disk/shares/Seqs/test_7942raw_2.fq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk1/202031107010094/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa

Multiple cores found: Using 4 threads

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1

        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:54)

        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)

        at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)

        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)

        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)