Hi guys, On our local galaxy install I'm getting the error below when I run tophat for illumina like this:
http://snag.gy/HsWyS.jpg Any ideas? Thanks, Greg Error: Dataset generation errors Dataset 27: Tophat for Illumina on data 15: deletions Tool execution generated the following error message: Error in tophat: tophat: option --no-closure-search not recognized for detailed help see http://tophat.cbcb.umd.edu/manual.html cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed': No such file or directory cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed': No such file or directory cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam': No such file or directory cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed': No such file or directory The tool produced the following additional output: TopHat v2.0.6 tophat -p 4 -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3 --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --segment-length 25 --min-segment-intron 50 --max-segment-intron 500000 /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome /home/galaxy/000/dataset_306.dat ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
