These are chat archives for nextflow-io/nextflow

23rd
Jun 2017
Alexander Mikheyev
@mikheyev
Jun 23 2017 07:54
I am trying to combine split paired end fastq files using phase, but somehow this is no producing any output. Why is that?
forward =  Channel
     .fromPath("data/reads/*R1*.fastq.gz")
     .splitFastq( file: true, by: params.chunkSize)

reverse =  Channel
     .fromPath("data/reads/*R2*.fastq.gz")
     .splitFastq( file: true, by: params.chunkSize)

forward.phase(reverse).subscribe{ println it }
Paolo Di Tommaso
@pditommaso
Jun 23 2017 08:02
phase needs a key on which elements must agree
you can do something like this
forward =  Channel
     .fromPath("data/reads/*R1*.fastq.gz")
     .map { file-> tuple( getPrefix(file), file ) }
     .splitFastq( file: true, by: params.chunkSize)
where getPrefix is a custom function know need to define to get a command matching prefix for the both read pair files
Alexander Mikheyev
@mikheyev
Jun 23 2017 08:25
got it -- thank you
LukeGoodsell
@LukeGoodsell
Jun 23 2017 08:28

Good morning!
I’m getting the below error when I try to run a nextflow script on an SGE cluster:

Command output:
  Error: cannot find Java or it's a wrong version -- please make sure that Java 7 or higher it's installed
  Note: Nextflow is trying to use the Java VM defined by the following environment variables:
   JAVA_CMD: /usr/lib/jvm/jre-1.8.0-openjdk/bin/java
   JAVA_HOME: /usr/lib/jvm/jre-1.8.0-openjdk

Looking at the nextflow source I see the error is arising from this command:

$JAVA_CMD -version 2>&1 | awk '/version/ {print $3}' | grep '"1\.[7|8]\..*"' > /dev/null
if [ $? -ne 0 ]; then
...

However, when I run the command on all my cluster’s nodes I get an exit status of 0:

$ pdsh -g cluster '/usr/lib/jvm/jre-1.8.0-openjdk/bin/java -version 2>&1 | awk '"'"'/version/ {print $3}'"'"' | grep '"'"'"1\.[7|8]\..*"'"'"' >/dev/null; echo $?'
ip-10-75-0-246: 0
ip-10-75-0-31: 0
ip-10-75-0-110: 0
ip-10-75-0-206: 0
login1: 0
ip-10-75-0-28: 0
ip-10-75-0-160: 0
ip-10-75-0-218: 0
ip-10-75-0-164: 0

Any idea what’s going wrong?

Paolo Di Tommaso
@pditommaso
Jun 23 2017 08:31
weird, please open an issue on GH including the output of /usr/lib/jvm/jre-1.8.0-openjdk/bin/java -version 2>&1
LukeGoodsell
@LukeGoodsell
Jun 23 2017 08:59
Done: #381