[2019-07-05 11:19:33] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:19:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:19:33] Checking for Bowtie index files (genome)..
[2019-07-05 11:19:33] Checking for reference FASTA file
[2019-07-05 11:19:33] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:19:38] Reading known junctions from GTF file
[2019-07-05 11:19:41] Preparing reads
	 left reads: min. length=150, max. length=150, 24579196 kept reads (1926 discarded)
	right reads: min. length=150, max. length=150, 24564328 kept reads (16794 discarded)
[2019-07-05 11:45:22] Building transcriptome data files /scratch/7534478.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:45:38] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:51:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:13:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:37:30] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:37:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:58:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:59:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:00:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:02:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:03:48] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:05:17] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:06:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:30:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:32:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:35:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:37:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:39:50] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:42:02] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:44:05] Searching for junctions via segment mapping
[2019-07-05 15:19:28] Retrieving sequences for splices
[2019-07-05 15:22:03] Indexing splices
[2019-07-05 15:23:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:24:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:25:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:26:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:28:00] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:29:07] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:30:03] Joining segment hits
[2019-07-05 15:35:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:37:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:39:06] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:40:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:42:15] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:43:36] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:44:49] Joining segment hits
[2019-07-05 15:51:13] Reporting output tracks
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[2019-07-05 17:03:46] A summary of the alignment counts can be found in /scratch/7534478.1.linga/tophat2/align_summary.txt
[2019-07-05 17:03:46] Run complete: 05:44:13 elapsed