[2019-07-03 17:27:42] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-03 17:27:42] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:27:42] Checking for Bowtie index files (genome)..
[2019-07-03 17:27:42] Checking for reference FASTA file
[2019-07-03 17:27:42] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:27:44] Reading known junctions from GTF file
[2019-07-03 17:27:47] Preparing reads
	 left reads: min. length=150, max. length=150, 31225266 kept reads (446 discarded)
	right reads: min. length=150, max. length=150, 31225621 kept reads (91 discarded)
[2019-07-03 17:49:02] Building transcriptome data files /scratch/7505696.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 17:49:11] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 17:52:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:05:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:18:55] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:18:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 18:44:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 18:49:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 18:55:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 19:01:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 19:06:36] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 19:10:20] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 19:12:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:44:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:51:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 19:57:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:03:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:10:14] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:14:48] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:17:05] Searching for junctions via segment mapping
[2019-07-04 02:15:02] Retrieving sequences for splices
[2019-07-04 02:16:09] Indexing splices
[2019-07-04 02:16:46] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:22:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:28:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 02:34:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 02:40:20] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 02:43:58] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 02:44:52] Joining segment hits
[2019-07-04 02:52:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:58:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 03:04:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 03:10:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 03:16:41] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 03:20:13] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 03:21:12] Joining segment hits
[2019-07-04 03:29:00] Reporting output tracks
-----------------------------------------------
[2019-07-04 04:06:21] A summary of the alignment counts can be found in /scratch/7505696.1.linga/tophat2/align_summary.txt
[2019-07-04 04:06:21] Run complete: 10:38:38 elapsed