[2019-07-17 19:14:24] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-17 19:14:24] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:14:26] Checking for Bowtie index files (genome)..
[2019-07-17 19:14:26] Checking for reference FASTA file
[2019-07-17 19:14:26] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:14:32] Reading known junctions from GTF file
[2019-07-17 19:14:35] Preparing reads
	 left reads: min. length=150, max. length=150, 63810604 kept reads (5738 discarded)
	right reads: min. length=150, max. length=150, 63800468 kept reads (15874 discarded)
[2019-07-17 20:18:20] Building transcriptome data files /scratch/7775060.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:18:38] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:24:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 21:13:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 22:05:58] Resuming TopHat pipeline with unmapped reads
[2019-07-17 22:05:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 23:54:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 00:09:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 00:25:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 00:41:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 00:56:56] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 01:09:06] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 01:14:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 03:28:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 03:46:02] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 04:03:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 04:21:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 04:38:26] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 04:53:58] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 05:04:07] Searching for junctions via segment mapping
[2019-07-18 17:15:52] Retrieving sequences for splices
[2019-07-18 17:18:33] Indexing splices
[2019-07-18 17:20:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 17:33:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 17:46:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 17:59:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 18:12:39] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 18:21:22] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 18:23:48] Joining segment hits
[2019-07-18 18:47:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 19:01:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 19:14:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 19:28:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 19:41:23] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 19:50:02] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 19:52:26] Joining segment hits
[2019-07-18 20:17:12] Reporting output tracks
-----------------------------------------------
[2019-07-18 22:25:30] A summary of the alignment counts can be found in /scratch/7775060.1.linga/tophat2/align_summary.txt
[2019-07-18 22:25:30] Run complete: 1 days 03:11:05 elapsed