Example command
TrimmomaticPE \
-threads 4 \
"/dev/shm/wdl/cromwell-executions/mlst/3614c5ff-8c3f-4a24-b8ad-44118ed58baf/call-trim/trim/1a1d2363-15c8-400e-9c12-0b094a391626/call-trimmomatic/shard-0/inputs/data/example/M
938 R1.fastq.gz" \
"/dev/shm/wdl/cromwell-executions/mlst/3614c5ff-8c3f-4a24-b8ad-44118ed58baf/call-trim/trim/1a1d2363-15c8-400e-9c12-0b094a391626/call-trimmomatic/shard-0/inputs/data/example/M
938 R2.fastq.gz" \
"M 938 _1.trimmed.fastq.gz" \
"M 938 _1.unpaired.gz" \
"M 938 _2.trimmed.fastq.gz" \
"M 938 _2.unpaired.gz" \
HEADCROP:2 \
ILLUMINACLIP:"/usr/share/trimmomatic/TruSeq3-PE-2.fa":2:20:12:1:true \
SLIDINGWINDOW:3:22 \
MINLEN:36 \
CROP:9999 \
TOPHRED33
stderr:
Picked up _JAVA_OPTIONS:
-Djava.io.tmpdir=/dev/shm/wdl/cromwell-executions/mlst/3614c5ff-8c3f-4a24-b8ad-44118ed58baf/call-trim/trim/1a1d2363-15c8-400e-9c12-0b094a391626/call-trimmomatic/shard-0/execution/tmp.XH2cjE
TrimmomaticPE: Started with arguments:
-threads 4
/dev/shm/wdl/cromwell-executions/mlst/3614c5ff-8c3f-4a24-b8ad-44118ed58baf/call-trim/trim/1a1d2363-15c8-400e-9c12-0b094a391626/call-trimmomatic/shard-0/inputs/data/example/M
938 R1.fastq.gz
/dev/shm/wdl/cromwell-executions/mlst/3614c5ff-8c3f-4a24-b8ad-44118ed58baf/call-trim/trim/1a1d2363-15c8-400e-9c12-0b094a391626/call-trimmomatic/shard-0/inputs/data/example/M
938 R2.fastq.gz M 938 _1.trimmed.fastq.gz M 938 _1.unpaired.gz M 938
_2.trimmed.fastq.gz M 938 _2.unpaired.gz HEADCROP:2
ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-PE-2.fa:2:20:12:1:true
SLIDINGWINDOW:3:22 MINLEN:36 CROP:9999 TOPHRED33
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: M
at
org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:67)
at
org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:41)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:529)
at org.usadellab.trimmomatic.TrimmomaticPE.main(TrimmomaticPE.java:540)
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https://bugs.launchpad.net/bugs/1702235
Title:
trimmomatic fails on spaces in filenames
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