Hi all,
I've run my RNA-Seq data through tophat for the rn5 genome and it worked as expected.
I wanted to compare it to some old data, and so I tried realigning to the rn4 genome. However, one of my samples failed. I tried rerunning it, and it failed again. I reset the computer, started galaxy and ran it without touching anything else and it failed again.
It's the same sample (I’ve imported it from shared data) that I ran last time. All 11 other samples worked for the rn5 alignment.
The error doesn't seem to be in the analysis, but in the reporting. The error I get in galaxy is:
[...] [2016-05-06 05:24:38] Indexing splicesBuilding a SMALL index
[2016-05-06 05:25:57] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2016-05-06 05:30:45] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2016-05-06 05:34:57] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2016-05-06 05:39:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2016-05-06 05:44:50] Joining segment hits
[2016-05-06 05:53:49] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2016-05-06 05:57:45] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2016-05-06 06:01:53] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2016-05-06 06:06:12] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2016-05-06 06:12:44] Joining segment hits
[2016-05-06 06:22:49] Reporting output tracks
[FAILED]
Error running /home/user/galaxy/toolbox/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 70 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 1000 --max-insertion-length 3 --max-deletion-length 3 -z gzip --inner-dist-mean 300 --inner-dist-std-dev 20 --no-closure-search --no-coverage-search --no-microexon-search --library-type fr-unstranded --sam-header ./tophat_out/tmp/rn4_genome.bwt.samheader.sam --report-mixed-alignments --samtools=/home/user/galaxy/toolbox/tophat/2.0.14/iuc/package_tophat_2_0_14/536f7bb5616d/bin/samtools_0.1.18 --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /home/user/galaxy/tool-data/rn4/bowtie2_index/rn4/rn4.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.mapped.bam,./tophat_out/tmp/left_kept_reads.candidates.bam ./tophat_out/tmp/left_kept_reads.bam ./tophat_out/tmp/right_kept_reads.mapped.bam,./tophat_out/tmp/right_kept_reads.candidates.bam ./tophat_out/tmp/right_kept_reads.bam
Loaded 201494 junctions
Which doesn't really tell me much. In the terminal it shows:
galaxy.jobs.runners.local DEBUG 2016-05-06 06:51:42,725 execution finished: /media/user/Storage/galaxy/job_working_directory/000/533/galaxy_533.sh
galaxy.jobs.output_checker INFO 2016-05-06 06:51:42,767 Job 533: Fatal error: Tool execution failed
galaxy.jobs DEBUG 2016-05-06 06:51:42,807 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-05-06 06:51:42,825 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-05-06 06:51:42,840 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-05-06 06:51:42,854 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-05-06 06:51:42,867 setting dataset state to ERROR
galaxy.jobs INFO 2016-05-06 06:51:43,010 Collecting job metrics for <galaxy.model.job object="" at="" 0x7f8974703150="">
galaxy.jobs DEBUG 2016-05-06 06:51:43,023 job 533 ended (finish() executed in (297.702 ms))
galaxy.datatypes.metadata DEBUG 2016-05-06 06:51:43,024 Cleaning up external metadata files
galaxy.datatypes.metadata DEBUG 2016-05-06 06:51:43,053 Failed to cleanup MetadataTempFile temp files from /media/user/Storage/galaxy/job_working_directory/000/533/metadata_out_HistoryDatasetAssociation_1874_EMhqTG: No JSON object could be decoded
I have more than enough RAM (125 GB), more than enough HD space (500 GB) and nothing else is going on during this time. If anybody has any insight, or additional places I could look to hunt down this error, I'd appreciate it greatly!
Thanks!
This is a local instance, so doesn't have anything to do with usegalaxy.org's recent problems.