[2019-07-04 03:20:30] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-04 03:20:30] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-04 03:20:30] Checking for Bowtie index files (genome)..
[2019-07-04 03:20:30] Checking for reference FASTA file
[2019-07-04 03:20:30] Generating SAM header for Bowtie2Index/genome
[2019-07-04 03:20:35] Reading known junctions from GTF file
[2019-07-04 03:20:39] Preparing reads
	 left reads: min. length=150, max. length=150, 32621150 kept reads (466 discarded)
	right reads: min. length=150, max. length=150, 32621535 kept reads (81 discarded)
[2019-07-04 03:57:01] Building transcriptome data files /scratch/7505715.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-04 03:57:21] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-04 04:04:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 04:23:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 04:43:59] Resuming TopHat pipeline with unmapped reads
[2019-07-04 04:43:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 06:14:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 06:24:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 06:34:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 06:45:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 06:55:27] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 07:02:40] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 07:06:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 08:06:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 08:17:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 08:28:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 08:40:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 08:51:08] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 08:59:13] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 09:03:30] Searching for junctions via segment mapping
[2019-07-04 14:52:22] Retrieving sequences for splices
[2019-07-04 14:54:42] Indexing splices
[2019-07-04 14:55:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 15:02:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 15:10:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 15:17:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 15:25:17] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 15:29:53] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 15:31:05] Joining segment hits
[2019-07-04 15:45:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 15:53:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 16:00:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 16:09:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 16:16:14] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 16:20:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 16:21:53] Joining segment hits
[2019-07-04 16:35:15] Reporting output tracks
-----------------------------------------------
[2019-07-04 17:30:59] A summary of the alignment counts can be found in /scratch/7505715.1.linga/tophat2/align_summary.txt
[2019-07-04 17:30:59] Run complete: 14:10:29 elapsed