trimmomatic fails on spaces in filenames

[Redmar]

There is an error in the wrapper for the java class, which means that properly quoted arguments (like "File name.extension") get expanded, and passed as File name.extension

from /usr/bin/TrimmomaticSE
# Original
#java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCTIONTOCALL $@
# Fixed
java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCTIONTOCALL "$@"

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: trimmomatic 0.35+dfsg-1
ProcVersionSignature: Ubuntu 4.4.0-83.106-generic 4.4.70
Uname: Linux 4.4.0-83-generic x86_64
NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
ApportVersion: 2.20.1-0ubuntu2.6
Architecture: amd64
CurrentDesktop: Unity
Date: Tue Jul 4 09:31:26 2017
EcryptfsInUse: Yes
InstallationDate: Installed on 2016-01-01 (549 days ago)
InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Alpha amd64 (20151209)
PackageArchitecture: all
SourcePackage: trimmomatic
UpgradeStatus: No upgrade log present (probably fresh install)

[Redmar (redmar)]

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)

[Hans Joachim Desserud (hjd)]

Thanks for reporting.

I took the liberty of attached a bug watch for the corresponding Debian report.

It looks like bug 1558602 covers the same issue, but it talks about two binaries (or rather binary wrappers). Will the suggested patch address both?

[Redmar (redmar)]

The suggested patch should address both. As I understand it, both wrappers link to the same file, which uses the name of the wrapper file to determine which part of the .jar to address.

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[Hans Joachim Desserud (hjd)]

>The suggested patch should address both.

Great :) I took the liberty of marking the other issue as a duplicate of this, then.

[Dylan Aïssi (daissi)]

Fixed in trimmomatic 0.36+dfsg-2, so since Artful.