Entering edit mode
5.1 years ago
F.I.2011 ▴ 10
I am new in Linux and Trimmomatic , do after installation i need to run it by any specific command I am using this command:
mohana@monash-Precision-T3600:~$ java -jar ~/Desktop/Farheena/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 8 -phred33 -trimlog FQ-1_log home/desktop/Farheena/41 FQ-1_R1_001.fastq.gz FQ-1_R2_001.fastq.gz home/Desktop/Farheena/41 FQ-1_1P.fq.gz FQ-1_1U.fq.gz FQ-1_2P.fq.gz FQ-1_2U.fq.qz ILLUMINACLIP:/home/mohana/Desktop/Farheena/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50^C
but getting this error:
TrimmomaticPE: Started with arguments: -threads 8 -phred33 -trimlog FQ-1_log home/desktop/Farheena/41 FQ-1_R1_001.fastq.gz FQ-1_R2_001.fastq.gz home/Desktop/Farheena/41 FQ-1_1P.fq.gz FQ-1_1U.fq.gz FQ-1_2P.fq.gz FQ-1_2U.fq.qz ILLUMINACLIP:/home/mohana/Desktop/Farheena/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: FQ-1_2P.fq.gz at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:70) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
please help me to sort out this puzzle
thanks for replying, i correct that mistake but then again it didn't solve my problem. It look like there are many script problems. i modified my command
and now getting this error:
Did you change the whitespace in the command only, or did you ALSO rename the files?
Are you in the correct folder?
thanks for helping, yes you caught the exact culprits... First i was not in correct folder. i went to FQ-1 folder second I have already been changed the name of input files but repeatedly using old command with old names.
I think i did it:
My lab mate mentioned that i should be in the same folder/directory where i put my both files (R1 and R2). might it will helped anyone else who is new in this field like me. But i didn't get Log file within folder FQ-1
That command option should have been
-trimlog FQ-1/FQ-1_logif you wanted to put the log file called
FQ-1_login the directory
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