Trimmomatic usage error( a little bit weird)

Question

[Decen]

Hi All, I am a newcomer in bioinformatics. recently I use the trimmomatic to train myself. First, I install the trimmomatic by conda(it is really a great software), which means I can execute by command line "trimmomatic PE -threads 4 -phred 33........(as the standard protocol)", it works but please below some errors happened: my question are: 1. why cannot find the TruSeq3-PE.fa? I found the file in ~/miniconda3/pkgs/trimmomatic-0.38-1/share/trimmomatic-0.38-1/adapters. 2. and the other problems as shown. error:

trimmomatic PE -phred33 SRR4449813_1_1.fastq SRR4449813_1_2.fastq paired_1_R1_paired.fq.gz unpaired_1_R1_unpaired.fq.gz paired_1_R2_paired.fq.gz unpaired_1_R2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:3

**TrimmomaticPE: Started with arguments:
 -phred33 SRR4449813_1_1.fastq SRR4449813_1_2.fastq paired_1_R1_paired.fq.gz unpaired_1_R1_unpaired.fq.gz paired_1_R2_paired.fq.gz unpaired_1_R2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:3
Multiple cores found: Using 4 threads
java.io.FileNotFoundException: /home/decen/下载/srr/TruSeq3-PE.fa (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71)
    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)
Input Read Pairs: 3438238 Both Surviving: 3397549 (98.82%) Forward Only Surviving: 37731 (1.10%) Reverse Only Surviving: 2828 (0.08%) Dropped: 130 (0.00%)
TrimmomaticPE: Completed successfully**

Thanks a lot!

[WouterDeCoster]

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Answer 1

[ATpoint]

For the part ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 to work, the adapter file has to be in the directory you are currently in. Either do ILLUMINACLIP:$HOME/miniconda3/pkgs/trimmomatic-0.38-1/share/trimmomatic-0.38-1/adaptersTruSeq3-PE.fa:2:30:10 or copy the adapter files to the current directory.

[Decen]

thanks, I found that problem and I crack it. Many thanks!

Answer 2

[Decen]

Thanks a lot! I think I have done it well. I should add "the adaptor file" into the sequence file (you wanna trim) or add the command "absolute path of the adaptor file in trimmomatic" following: ILLUMINACLIP: absolute path of adaptor file