using trimmomatic software

Question

[haddadfatiha62]

Hi I m begening at bioinformatic ,i want use trimmomatic for trimming my data , i install trimmomatic by conda , and i use this command

trimmomatic PE -phred33 ERR770964_1.fastq ERR770964_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 MIN

i get 4output paired and un paired (reverse and forward) but i also get this message, i didn't know if my trimming is correct or no ,how I can verify my trimming??

TrimmomaticPE: Started with arguments:
 -phred33 ERR770964_1.fastq ERR770964_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
java.io.FileNotFoundException: /data/f.haddad/analyses/TruSeq3-PE.fa (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        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: 1151860 Both Surviving: 1143620 (99.28%) Forward Only Surviving: 8157 (0.71%) Reverse Only Surviving: 75 (0.01%) Dropped: 8 (0.00%)TrimmomaticPE: Completed successfully

can you help me please

[swbarnes2]

FileNotFoundException: /data/f.haddad/analyses/TruSeq3-PE.fa (No such file or directory)

Doesn't that suggest that something didn't work correctly? Are you absolutely sure that there is a file by that name in that location?

[lieven.sterck]

hi haddadfatiha62 ,

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Answer 1

[evoBio]

Its not finding the adapter sequence file TruSeq3-PE.fa. Adapter sequence files are in the adapters folder within the Trimmomatic folder. You should provide the correct path to that adapter .fa file in your command as shown below.

ILLUMINACLIP: path to your trimmomatic folder/adapters/TruSeq3-PE.fa

Answer 2

[haddadfatiha62]

yes you are right Ihave a problem in the path of the directory thanks you so much for your help