error in execution of Trimmomatic 0.36

Question

[F.I.2011]

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

[F.I.2011]

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)

[Matteo Schiavinato]

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?

[F.I.2011]

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.

[F.I.2011]

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

[GenoMax]

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.

[GenoMax]

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.

Answer 1

[Matteo Schiavinato]

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:

• remove the whitespace from the path, by renaming the files / folders that contain it (highly recommended)
• add a \ before each whitespace to "escape" it (see https://en.wikipedia.org/wiki/Escape_character)

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!

[kloetzl]

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