Trimmomatic output file Issue

Question

[akh22]

Hi,

Using brew installed trimmomatic/0.38 and run a following script;

java -Xms4000M -Xmx12000m -XX:+UseConcMarkSweepGC \
        -XX:NewSize=300M -XX:MaxNewSize=300M \
        -jar /usr/local/Cellar/trimmomatic/0.38/libexec/trimmomatic-0.38.jar \
        PE -threads 24 -trimlog sample1_R1_001.fastq.gz  Sample2_R2_001.fastq.gz\
        ~/Desktop/output_forward_paired.fq.gz ~/Desktop/output_forward_unpaired.fq.gz\
        ~/Desktop/output_reverse_paired.fq.gz ~/Desktop/output_reverse_unpaired.fq.gz\
        ILLUMINACLIP:/usr/local/Cellar/trimmomatic/0.38/share/trimmomatic/adapters/TruSeq3-PE-2.fa:2:30:10\
        LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

I get this an error code;

Exception in thread "main" java.io.FileNotFoundException: /Volumes/Documents/ahoji/Desktop/output_forward_paired.fq.gz (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:213)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:155)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:268)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

I though this might be the file permission issue and I changed output directories to different directories but I still get the same error. I'd really appreciate any help on this.

Thanks in advance.

java -version java version "12.0.1" 2019-04-16 Java(TM) SE Runtime
Environment (build 12.0.1+12) Java HotSpot(TM) 64-Bit Server VM (build
12.0.1+12, mixed mode, sharing)


sw_vers
ProductName:    Mac OS X
ProductVersion: 10.14.5
BuildVersion:   18F132

[lshepard]

What happens if you remove the ~/Desktop/ from all the output files? I believe Trimmomatic outputs the files in the current working directory.

[manuel.belmadani]

As a quick sanity check, can you check that /Volumes/Documents/ahoji/Desktop/ exists?

i.e. ls /Volumes/Documents/ahoji/Desktop/

[akh22]

Thanks for all the suggestions, though Damian's comment fixed it. I completely missed trimlog location and after specifying the location, it run just fine. Luckily, trimmomatic did not run completely to erase fastqs.

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Answer 1

[Damian Kao]

It looks like you are not specifying an output file for the -trimlog parameter. So it thinks your output_forward_paired.fq.gz is an input.

I hope you still can still redownload sample1_R1_001.fastq.gz, because it might have been overwritten.