[2019-07-11 10:32:19] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-11 10:32:19] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-11 10:32:19] Checking for Bowtie index files (genome)..
[2019-07-11 10:32:19] Checking for reference FASTA file
[2019-07-11 10:32:19] Generating SAM header for Bowtie2Index/genome
[2019-07-11 10:32:27] Reading known junctions from GTF file
[2019-07-11 10:32:30] Preparing reads
	 left reads: min. length=151, max. length=151, 71514977 kept reads (4689 discarded)
	right reads: min. length=151, max. length=151, 71503209 kept reads (16457 discarded)
[2019-07-11 11:55:03] Building transcriptome data files /scratch/7655515.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-11 11:55:39] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-11 12:05:27] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-11 13:13:48] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-11 14:29:22] Resuming TopHat pipeline with unmapped reads
[2019-07-11 14:29:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-11 17:15:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-11 17:49:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-11 18:24:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-11 18:59:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-11 19:34:41] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-11 20:04:37] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-11 20:27:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-11 23:09:53] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-11 23:47:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 00:25:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 01:04:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 01:43:18] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 02:16:21] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 02:41:58] Searching for junctions via segment mapping
[2019-07-12 04:00:37] Retrieving sequences for splices
[2019-07-12 04:02:40] Indexing splices
[2019-07-12 04:03:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 04:19:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 04:33:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 04:47:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 05:02:52] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 05:15:26] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 05:24:04] Joining segment hits
[2019-07-12 06:03:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-12 06:20:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-12 06:36:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-12 06:52:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-12 07:08:37] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-12 07:21:58] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-12 07:31:22] Joining segment hits
[2019-07-12 08:15:21] Reporting output tracks
-----------------------------------------------
[2019-07-12 11:03:58] A summary of the alignment counts can be found in /scratch/7655515.1.linga/tophat2/align_summary.txt
[2019-07-12 11:03:58] Run complete: 1 days 00:31:39 elapsed