[2014-05-29 02:54:12] Beginning TopHat run (v2.0.8b) ----------------------------------------------- [2014-05-29 02:54:12] Checking for Bowtie Bowtie version: 2.1.0.0 [2014-05-29 02:54:12] Checking for Samtools Samtools version: 0.1.19.0 [2014-05-29 02:54:12] Checking for Bowtie index files [2014-05-29 02:54:12] Checking for reference FASTA file [2014-05-29 02:54:12] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10 format: fastq quality scale: phred33 (default) [2014-05-29 02:54:14] Preparing reads left reads: min. length=60, max. length=101, 23139584 kept reads (1880 discarded) [2014-05-29 03:04:33] Mapping left_kept_reads to genome mm10 with Bowtie2 [2014-05-29 03:45:38] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4) [2014-05-29 03:48:48] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4) [2014-05-29 03:52:24] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4) [2014-05-29 03:56:05] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4) [2014-05-29 03:59:44] Searching for junctions via segment mapping [2014-05-29 04:08:46] Retrieving sequences for splices [2014-05-29 04:10:45] Indexing splices [2014-05-29 04:11:38] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4) [2014-05-29 04:13:29] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4) [2014-05-29 04:15:42] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4) [2014-05-29 04:17:45] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4) [2014-05-29 04:19:40] Joining segment hits [2014-05-29 04:23:20] Reporting output tracks ----------------------------------------------- [2014-05-29 04:36:51] Run complete: 01:42:39 elapsed