[2019-06-28 13:26:34] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:26:34] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:26:34] Checking for Bowtie index files (genome)..
[2019-06-28 13:26:34] Checking for reference FASTA file
[2019-06-28 13:26:34] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:26:40] Reading known junctions from GTF file
[2019-06-28 13:26:44] Preparing reads
	 left reads: min. length=150, max. length=150, 22865334 kept reads (344 discarded)
	right reads: min. length=150, max. length=150, 22865578 kept reads (100 discarded)
[2019-06-28 13:53:52] Building transcriptome data files /scratch/7287273.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:54:10] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 14:01:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:26:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:52:23] Resuming TopHat pipeline with unmapped reads
[2019-06-28 14:52:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 15:38:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 15:45:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 15:52:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 15:59:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:07:06] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:14:30] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:18:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 17:03:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:11:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:19:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:27:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 17:34:35] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 17:40:40] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 17:44:00] Searching for junctions via segment mapping
[2019-06-28 23:17:10] Retrieving sequences for splices
[2019-06-28 23:20:00] Indexing splices
[2019-06-28 23:21:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-28 23:26:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-28 23:31:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-28 23:35:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-28 23:41:15] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-28 23:45:12] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-28 23:46:18] Joining segment hits
[2019-06-28 23:57:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 00:02:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 00:08:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 00:15:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 00:21:35] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 00:25:44] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 00:26:58] Joining segment hits
[2019-06-29 00:40:03] Reporting output tracks
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[2019-06-29 01:45:45] A summary of the alignment counts can be found in /scratch/7287273.1.linga/tophat2/align_summary.txt
[2019-06-29 01:45:45] Run complete: 12:19:11 elapsed