[2019-06-28 13:26:43] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:26:43] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:26:44] Checking for Bowtie index files (genome)..
[2019-06-28 13:26:44] Checking for reference FASTA file
[2019-06-28 13:26:44] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:26:47] Reading known junctions from GTF file
[2019-06-28 13:26:51] Preparing reads
	 left reads: min. length=150, max. length=150, 19686311 kept reads (307 discarded)
	right reads: min. length=150, max. length=150, 19686528 kept reads (90 discarded)
[2019-06-28 13:51:01] Building transcriptome data files /scratch/7287278.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:51:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 13:58:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:16:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:36:34] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:36:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:13:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:18:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:23:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:28:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 15:33:41] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 15:38:00] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 15:40:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:18:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:23:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:28:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:34:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:40:01] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:45:15] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:47:58] Searching for junctions via segment mapping
[2019-06-28 19:57:52] Retrieving sequences for splices
[2019-06-28 20:00:18] Indexing splices
[2019-06-28 20:01:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:03:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:06:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:09:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:12:36] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:14:51] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:15:36] Joining segment hits
[2019-06-28 20:23:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 20:26:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 20:29:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 20:32:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 20:35:33] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 20:37:42] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 20:38:27] Joining segment hits
[2019-06-28 20:46:56] Reporting output tracks
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[2019-06-28 21:42:10] A summary of the alignment counts can be found in /scratch/7287278.1.linga/tophat2/align_summary.txt
[2019-06-28 21:42:10] Run complete: 08:15:27 elapsed