[2019-07-12 13:50:16] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:50:16] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:50:16] Checking for Bowtie index files (genome)..
[2019-07-12 13:50:16] Checking for reference FASTA file
[2019-07-12 13:50:16] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:50:22] Reading known junctions from GTF file
[2019-07-12 13:50:25] Preparing reads
	 left reads: min. length=151, max. length=151, 55448350 kept reads (105 discarded)
	right reads: min. length=151, max. length=151, 55442724 kept reads (5731 discarded)
[2019-07-12 14:54:54] Building transcriptome data files /scratch/7678204.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:55:11] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:01:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:31:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:10:10] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:10:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 18:25:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 18:53:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 19:20:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 19:50:56] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 20:19:31] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 20:42:39] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 21:01:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 23:46:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 00:17:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 00:47:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 01:18:47] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 01:49:15] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 02:14:39] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 02:37:33] Searching for junctions via segment mapping
[2019-07-13 03:19:19] Retrieving sequences for splices
[2019-07-13 03:21:54] Indexing splices
[2019-07-13 03:22:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 03:57:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 04:33:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 05:07:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 05:40:08] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 06:05:38] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 06:19:20] Joining segment hits
[2019-07-13 07:10:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 07:51:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 08:28:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 09:01:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 09:33:03] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 09:58:07] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 10:13:05] Joining segment hits
[2019-07-13 11:01:16] Reporting output tracks
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[2019-07-13 12:18:01] A summary of the alignment counts can be found in /scratch/7678204.1.linga/tophat2/align_summary.txt
[2019-07-13 12:18:01] Run complete: 22:27:44 elapsed