error in execution of Trimmomatic 0.36
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3.2 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 software error • 2.5k views ADD COMMENT 0 Entering edit mode 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  java -jar ~/Desktop/Farheena/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 4 -phred33 -trimlog FQ-1_log FQ-1_S56_L001_R1_001.fastq FQ-1_S56_L001_R2_001.fastq FQ-1_forward_paired.fq.gz FQ-1_forward_unpaired.fq.gz FQ-1_reverse_paired.fq.gz FQ-1_reverse_unpaired.fq.gz ILLUMINACLIP:/home/mohana/Desktop/Farheena/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  and now getting this error: TrimmomaticPE: Started with arguments: -threads 4 -phred33 -trimlog FQ-1_log FQ-1_S56_L001_R1_001.fastq FQ-1_S56_L001_R2_001.fastq FQ-1_forward_paired.fq.gz FQ-1_forward_unpaired.fq.gz FQ-1_reverse_paired.fq.gz FQ-1_reverse_unpaired.fq.gz ILLUMINACLIP:/home/mohana/Desktop/Farheena/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Exception in thread "main" java.io.FileNotFoundException: FQ-1_S56_L001_R1_001.fastq (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.fastq.FastqParser.parse(FastqParser.java:135) at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:264) at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:539) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)  ADD REPLY 0 Entering edit mode java.io.FileNotFoundException: FQ-1_S56_L001_R1_001.fastq (No such file or directory) Did you change the whitespace in the command only, or did you ALSO rename the files? Are you in the correct folder? ADD REPLY 0 Entering edit mode 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. ADD REPLY 0 Entering edit mode I think i did it: ~/Desktop/Farheena/41 /FQ-1$ java -jar ~/Desktop/Farheena/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 4 -phred33 -trimlog FQ-1_log FQ-1_R1_001.fastq FQ-1_R2_001.fastq FQ-1_forward_paired.fq FQ-1_forward_unpaired.fq FQ-1_reverse_paired.fq FQ-1_reverse_unpaired.fq ILLUMINACLIP:/home/mohana/Desktop/Farheena/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
TrimmomaticPE: Started with arguments:
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 8216 Both Surviving: 2456 (29.89%) Forward Only Surviving: 5488 (66.80%) Reverse Only Surviving: 20 (0.24%) Dropped: 252 (3.07%)


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

-trimlog FQ-1_log

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Entering edit mode

That command option should have been -trimlog FQ-1/FQ-1_log if you wanted to put the log file called FQ-1_log in the directory FQ-1.

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farheena.iqbal : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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3.2 years ago
Macspider ★ 3.4k

You have a whitespace in your path:

home/desktop/Farheena/41 FQ-1_R1_001.fastq.gz


Between 41 and FQ-1_R1_001.fastq.gz. Command line arguments have a hard time handling whitespaces, but you're excused since you're new to Linux :) you have 2 solutions:

I know the second option is tempting, but you really need to learn not to use whitespaces as soon as possible so go for the first!

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Third option: Use quotes: "home/desktop/Farheena/41 FQ-1_R1_001.fastq.gz"