21-4-Trimmomatic安装运行

1.输入unzip命令行提示“ubuntu 环境变量失效”

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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

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解决方法:将/usr/bin写入环境变量

export PATH=/usr/bin:$PATH

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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

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Usage:

      PE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] [-validatePairs] [-basein | ] [-baseo                                                                                      ut | ] ...

  or:

      SE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] ...

  or:

      -version

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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

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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

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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)

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