[2019-07-03 19:26:43] Beginning TopHat run (v2.1.1)
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[2019-07-03 19:26:43] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 19:26:43] Checking for Bowtie index files (genome)..
[2019-07-03 19:26:43] Checking for reference FASTA file
[2019-07-03 19:26:43] Generating SAM header for Bowtie2Index/genome
[2019-07-03 19:26:45] Reading known junctions from GTF file
[2019-07-03 19:26:49] Preparing reads
	 left reads: min. length=150, max. length=150, 31965214 kept reads (430 discarded)
	right reads: min. length=150, max. length=150, 31965555 kept reads (89 discarded)
[2019-07-03 20:03:03] Building transcriptome data files /scratch/7505709.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 20:03:21] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 20:10:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 20:29:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 20:49:29] Resuming TopHat pipeline with unmapped reads
[2019-07-03 20:49:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 21:49:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 21:58:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 22:08:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:17:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:26:38] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:32:43] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 22:36:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 23:43:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 23:53:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 00:03:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 00:14:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 00:25:00] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 00:32:47] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 00:36:59] Searching for junctions via segment mapping
[2019-07-04 04:38:03] Retrieving sequences for splices
[2019-07-04 04:40:29] Indexing splices
[2019-07-04 04:41:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 04:48:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 04:54:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 05:01:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 05:07:21] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 05:11:11] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 05:12:23] Joining segment hits
[2019-07-04 05:26:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 05:34:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 05:42:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 05:49:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 05:56:07] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 06:00:42] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 06:02:08] Joining segment hits
[2019-07-04 06:16:28] Reporting output tracks
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[2019-07-04 07:08:12] A summary of the alignment counts can be found in /scratch/7505709.1.linga/tophat2/align_summary.txt
[2019-07-04 07:08:12] Run complete: 11:41:29 elapsed