Entering edit mode
3.0 years ago
Xiaoyun
▴
10
Hi all,
I am really struggling with Trimmomatic these days and getting confused. I'm trying to run trimmomatic:
java -jar trimmomatic-0.39.jar PE -threads 2 -phred33 \ ly1_1.fq ly1_2.fq \ ly1_paired_1.trimmed.fq ly1_unpaired_1.trimmed.fq ly1_paired_2.trimmed.fq ly1_unpaired_2.trimmed.fq HEADCROP:9
This is my error:
TrimmomaticPE: Started with arguments:`
-threads 2 -phred64 ly1_1.fq ly1_2.fq ly1_paired_1.trimmed.fq ly1_unpaired_1.trimmed.fq ly1_paired_2.trimmed.fq ly1_unpaired_2.trimmed.fq HEADCROP:9
Exception in thread "main" java.io.FileNotFoundException: ly1_1.fq (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:265)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
Any help would be appreciated.
Thank you so much!
But it exactly exists in my mobile HDD.
Are the reads files located within your working directory? Try providing the full paths to the reads files.
I have fixed that. But when I input the command:
This is another error:
Not sure what your issue is then. I installed trimmomatic via conda and ran the following, which worked:
I also tried a simplified version, which worked:
Thanks a lot! I think I have done it well.
I think maybe there is something wrong in output file name.
I'm wondering if it is anything to do with the
\
charactors you have in there. That is I wonder if my using\
you are forcing it to include the following space in the name of the trimmer. So it is looking for " HEADCROP" rather than "HEADCROP"