1.輸入unzip命令行提示“ubuntu 環(huán)境變量失效”

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

解決方法:將/usr/bin寫入環(huán)境變量

export PATH=/usr/bin:$PATH

最后顯示

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

成功運(yùn)行

2.運(yùn)行測(cè)試

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

同樣成功

3.原始數(shù)據(jù)過濾

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后的路徑換為自己的，用相對(duì)路徑就出錯(cuò)了

替換后即為：

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

顯示為

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)