[2019-07-03 18:08:35] Beginning TopHat run (v2.1.1)
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[2019-07-03 18:08:35] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 18:08:36] Checking for Bowtie index files (genome)..
[2019-07-03 18:08:36] Checking for reference FASTA file
[2019-07-03 18:08:36] Generating SAM header for Bowtie2Index/genome
[2019-07-03 18:08:39] Reading known junctions from GTF file
[2019-07-03 18:08:42] Preparing reads
	 left reads: min. length=150, max. length=150, 29185161 kept reads (385 discarded)
	right reads: min. length=150, max. length=150, 29185468 kept reads (78 discarded)
[2019-07-03 18:37:29] Building transcriptome data files /scratch/7505705.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 18:37:44] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 18:43:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:00:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 19:17:42] Resuming TopHat pipeline with unmapped reads
[2019-07-03 19:17:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 20:10:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 20:18:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 20:26:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:35:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:43:49] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:49:22] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:52:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 21:50:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 21:59:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:08:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:17:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:27:12] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:34:06] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 22:38:03] Searching for junctions via segment mapping
[2019-07-04 00:45:07] Retrieving sequences for splices
[2019-07-04 00:47:21] Indexing splices
[2019-07-04 00:48:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 00:52:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 00:56:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 01:00:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 01:04:33] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 01:07:07] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 01:07:59] Joining segment hits
[2019-07-04 01:18:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 01:22:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 01:26:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 01:31:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 01:35:07] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 01:37:39] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 01:38:36] Joining segment hits
[2019-07-04 01:49:08] Reporting output tracks
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[2019-07-04 02:29:13] A summary of the alignment counts can be found in /scratch/7505705.1.linga/tophat2/align_summary.txt
[2019-07-04 02:29:13] Run complete: 08:20:37 elapsed