Hello, I don't know why I still have this problem.. I have run tophat2 with different dataset, sometimes it goes well but sometime I have this error.

I run only one job at a time on a virtual machine with 8G memory without using galaxy plateform. I tried --no-coverage-search option but it changes nothing.

Thanks. Delong ------------------------------------------------------------------------ *De :* Delong, Zhou *Envoyé :* 27 août 2013 9:36 *À :* galaxy-user(a)bx.psu.edu *Objet :* Tophat Error: segment-based junction search failed with err Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2013-08-23 11:56:58] Checking for Bowtie Bowtie version: 2.0.2.0 [2013-08-23 11:56:58] Checking for Samtools Samtools version: 0.1.18.0 [2013-08-23 11:56:58] Checking for Bowtie index files [2013-08-23 11:56:58] Checking for reference FASTA file [2013-08-23 11:56:58] Generating SAM header for /usr/local/data/bowtie2/hg19/hg19 format: fastq quality scale: phred33 (default) [2013-08-23 11:58:04] Preparing reads left reads: min. length=50, max. length=50, 145339247 kept reads (34946 discarded) right reads: min. length=50, max. length=50, 145340153 kept reads (34040 discarded) [2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2 [2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2 [2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/2) [2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/2) [2013-08-25 01:40:37] Searching for junctions via segment mapping Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory. [FAILED] Error: segment-based junction search failed with err =-9 Collecting potential splice sites in islands cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed': No such file or directory cp: cannot stat `/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed': No such file or directory I did some research on the internet and it seems to be a memory problem to me, is there any solution other than rerun these jobs on a more powerful machine? And why has Bowtie/Tophat discard different numbers of reads? What will be the impact? Does it means that if I don't have exact matches between the paired end input, it is still be possible to run the job? Thanks, Delong ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/