Trimmomatic-0.36 is generating empty files

Question

[madzayasodara]

Hi, I'm running the following:

java -jar /home/madzays/bin/trimmomatic.jar PE -phred33 /home/madzays/data/finch_data/firstrun/test/RSFV1M_S47_L006_R1_001.fastq /home/madzays/data/finch_data/firstrun/test/RSFV1M_S47_L006_R2_001.fastq ./RSFV1M_S47_L006_R1_001_paired.fastq ./RSFV1M_S47_L006_R1_001_unpaired.fastq ./RSFV1M_S47_L006_R2_001_paired.fastq ./RSFV1M_S47_L006_R2_001_unpaired.fastq SLIDINGWINDOW:4:25 MINLEN:36

the programs seems to run:

TrimmomaticPE: Started with arguments: -phred33 /home/madzays/data/finch_data/firstrun/test/RSFV1M_S47_L006_R1_001.fastq /home/madzays/data/finch_data/firstrun/test/RSFV1M_S47_L006_R2_001.fastq ./RSFV1M_S47_L006_R1_001_paired.fastq ./RSFV1M_S47_L006_R1_001_unpaired.fastq ./RSFV1M_S47_L006_R2_001_paired.fastq ./RSFV1M_S47_L006_R2_001_unpaired.fastq SLIDINGWINDOW:4:25 MINLEN:36
Multiple cores found: Using 16 threads
Input Read Pairs: 0 Both Surviving: 0 (�%) Forward Only Surviving: 0 (�%) Reverse Only Surviving: 0 (�%) Dropped: 0 (�%)
TrimmomaticPE: Completed successfully

However,. all outputs are generated but empty. Any ideas what I might be going wrong? Thanks!

[lechu]

You did not provide any information on the input files. Without this, it is much harder to diagnose the problem.

[madzayasodara]

Input files are from PCR-free libraries Kapa Hyper, using TruSeq adapters, and run on HS4000 PE150 lanes. thanks! I am trying to run this in a shared cluster without root access though. When I run on my PC it works just fine.

Answer 1

[GenoMax]

./RSFV1M_S47_L006_R1_001_paired.fastq

Where is ./ pointing to? Do you have write permissions in that directory? This is where things are a bit confusing since you state that output files are created but are empty. Does the program seem to end right away? If it does then perhaps it is not able to read the source files from your home directory.

[madzayasodara]

Yep! That was the problem.