Question: error in execution of Trimmomatic 0.36
0
gravatar for F.I.2011
10 months ago by
F.I.201110
F.I.201110 wrote:

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 • 943 views
ADD COMMENTlink modified 10 months ago by genomax59k • written 10 months ago by F.I.201110

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 REPLYlink modified 10 months ago by genomax59k • written 10 months ago by F.I.201110

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 REPLYlink modified 10 months ago • written 10 months ago by Macspider2.6k

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 REPLYlink modified 10 months ago • written 10 months ago by F.I.201110

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:
 -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
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
ADD REPLYlink modified 10 months ago by genomax59k • written 10 months ago by F.I.201110

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.

If you are serious about learning basics of UNIX for biologists then spend a couple of hours at this link.

ADD REPLYlink written 10 months ago by genomax59k

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

All of your comments should have gone under @Macspider's answer.

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax59k
1
gravatar for Macspider
10 months ago by
Macspider2.6k
Vienna - BOKU
Macspider2.6k wrote:

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!

ADD COMMENTlink written 10 months ago by Macspider2.6k

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

ADD REPLYlink written 10 months ago by kloetzl990
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