I ran trimmomatic on my 100bp paired end Illumina hiseq dataset using the command below. But the output files were all empty when unzipped (4kb when zipped). The program ran for around 8 hours (each of the input fastq files is around 33gb) and the trimlog file was populated (11.19gb total), but it looks like every line indicates that the sequence length for each respective read is 0 (e.g. HS4_80:8:2308:9999:99196/2 0 0 0 0). I don't think the problem is with the input files since they pass qc.
Any ideas on what's going wrong?
nohup java -classpath trimmomatic-0.17.jar org.usadellab.trimmomatic.TrimmomaticPE -trimlog trimlog C08DRACXX.8_1.fastq C08DRACXX.8_2.fastq forward_paired.fq.gz forward_unpaired.fq.gz reverse_paired.fq.gz reverse_unpaired.fq.gz ILLUMINACLIP:adapters+RC_NOindexes_for_trimmomatic.fastq:2:40:15 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:70 &
Any ideas on what's going wrong?
nohup java -classpath trimmomatic-0.17.jar org.usadellab.trimmomatic.TrimmomaticPE -trimlog trimlog C08DRACXX.8_1.fastq C08DRACXX.8_2.fastq forward_paired.fq.gz forward_unpaired.fq.gz reverse_paired.fq.gz reverse_unpaired.fq.gz ILLUMINACLIP:adapters+RC_NOindexes_for_trimmomatic.fastq:2:40:15 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20 MINLEN:70 &
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