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YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
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Error in analyze_rna_seq.scala after updates #84

Closed ecwheele closed 8 years ago

ecwheele commented 8 years ago

I did a git pull in gscripts and that went fine, but running the pipeline gives the following error: https://gist.github.com/ecwheele/5af7e4e2ace5d398120d

My submission script looks like this:

NAME=mds_splicing
VERSION=v4
java -Xms512m -Xmx512m -jar /home/yeo-lab/software/gatk/dist/Queue.jar -S ~/gscripts/qscripts/analyze_rna_seq.scala --input manifest.txt --adapter TCGTATGCCGTCTTCTGCTTG --adapter ATCTCGTATGCCGTCTTCTGCTTG --adapter CGACAGGTTCAGAGTTCTACAGTCCGACGATC --adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -qsub -jobQueue home-scrm -log ${NAME}_${VERSION}.log --location /oasis/tscc/scratch/ecwheele/mds_splicing_v4/ --strict -keepIntermediates --flipped flip -run
ecwheele commented 8 years ago

Problem - Trailing white space at the end of the manifest file. Fixed. Thanks Gabe!