Trimmomatic job won't end

Question

[James Clark]

Hi,

I am trying to trim some reads Ive been given. I am trying to run it on several hundred paired end reads. These are kept in directories so that the directory "samples" contains each patient ID, which contains the forward and reverse fastq.gz files.

I am using a submit script, the arguments provided therefore are ${1} is the patient ID and ${2} is the code for the fastq.gz file.

The script I have is:

FASTQ_DIR="Path to samples"/samples/${1}
OUT_DIR="Path to out"/TRIM/${1}

mkdir -p ${OUT_DIR}

module add Java/1.8.0_144

java -jar /"Path to software"/software/Trimmomatic-0.39/trimmomatic-0.39.jar PE \
-phred33 \
${FASTQ_DIR}/${2}_R1_001.fastq.gz \
${FASTQ_DIR}/${2}_R2_001.fastq.gz \
-baseout ${OUT_DIR}/${2}.fastq.gz \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
LEADING:3 \
TRAILING:3 \
SLIDINGWINDOW:4:15 \
MINLEN:36

What happens then if I execute the script:

$ . TRIM.sh "PatientID" "SampleID"

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch
TrimmomaticPE: Started with arguments:
 -phred33 "Path to first fastq" "Path to second fastq" -baseout "Path to out" ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences

It then stays here indefinitely and just won't do anything else until I cancel it. It created the output files but they aren't correct and appear corrupted.

Any advice would be greatly appreciated here, I'm not great at bioinformatics so any explanation would be welcomed. Obviously I took out the patientID etc..

Thanks

[ATpoint]

Can you check with top if the job is running or not, so if it is simply a problem with exiting the process? Are you on a cluster with a scheduler?

[James Clark]

Hi, thanks for your response, Top shows the process running, it will run for an amount of time (usually a few minuets) then disappear and give a file that "ends unexpectedly" If I run it on my own screen it will never exit the job. Im on a cluster that uses Slurm workload manager. Thank you

[GenoMax]

Are FASTQ_DIR and OUT_DIR both available on the node where the job is being run?

[rasoulfarzaneh]

The script I have is

/Downloads/Trimmomatic-0.36$ java -jar trimmomatic-0.36.jar SE '/home/rasoul/Desktop/Data/ngs/SRR941816_fastqc.zip' /home/rasoul/Desktop/Data/ngs/SRR941816/keep.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10‬‬ ‫‪TRAILING:20‬‬ ‫‪SLIDINGWINDOW:6:20‬‬ ‫‪MINLEN:35

What happens then if I execute the script:

TrimmomaticSE: Started with arguments:
 /home/rasoul/Desktop/Data/ngs/SRR941816_fastqc.zip /home/rasoul/Desktop/Data/ngs/SRR941816/keep.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10‬‬ ‫‪TRAILING:20‬‬ ‫‪SLIDINGWINDOW:6:20‬‬ ‫‪MINLEN:35
Automatically using 4 threads
Exception in thread "main" java.lang.NumberFormatException: For input string: "10‬‬"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:580)
    at java.lang.Integer.parseInt(Integer.java:615)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:56)
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
    at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
    at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:303)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

[Ram]

How is this an answer to the top-level question? If this is not an answer, it should be either a comment or a new question.