Hi all,
Each time I try and run trimmomatic on my data it fails, having run successfully on my first few files a few days ago - what could I be doing wrong, why would it fail?
The message I get is:
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/040/883/40883757/_job_tmp -Xmx28g -Xms256m
TrimmomaticPE: Started with arguments:
-threads 6 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unp
Hi @storrsarah,
not enough information for helpful answer. What server do you use? The tool might fail because of user or ‘server’. Re-submit one of the previously completed jobs using Re-run bottom in Extended view. Does it fail? If yes, it is a strong indication the issue is caused by ‘server’ (software, hardware, transfer etc). Report the error to server admins. If it completes, input files or job setup are the prime suspects. Have you QC the reads? FastQC is a good option. Make sure the input files are from the same sample.
Kind regards,
Igor
FAQs
Note: For reference only – please follow the instructions @igor suggested and you will likely find the problem. If the problem continues, follow the guides below to report more information so we can help you!
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