[2019-07-12 13:50:16] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:50:16] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:50:16] Checking for Bowtie index files (genome)..
[2019-07-12 13:50:16] Checking for reference FASTA file
[2019-07-12 13:50:16] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:50:21] Reading known junctions from GTF file
[2019-07-12 13:50:25] Preparing reads
	 left reads: min. length=151, max. length=151, 67887327 kept reads (103 discarded)
	right reads: min. length=151, max. length=151, 67880293 kept reads (7137 discarded)
[2019-07-12 15:11:46] Building transcriptome data files /scratch/7678205.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:12:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:20:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:01:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:50:01] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:50:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:32:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 20:05:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:37:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:12:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:45:50] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:10:01] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 22:27:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:08:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:45:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:23:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 03:59:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:33:46] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:02:12] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:25:12] Searching for junctions via segment mapping
[2019-07-13 06:20:44] Retrieving sequences for splices
[2019-07-13 06:23:12] Indexing splices
[2019-07-13 06:23:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 07:06:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 07:56:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 08:36:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 09:14:29] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 09:43:36] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 09:57:48] Joining segment hits
[2019-07-13 10:53:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 11:33:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 12:14:57] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 12:54:14] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 13:32:37] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 14:02:00] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 14:17:57] Joining segment hits
[2019-07-13 15:13:20] Reporting output tracks
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[2019-07-13 16:43:12] A summary of the alignment counts can be found in /scratch/7678205.1.linga/tophat2/align_summary.txt
[2019-07-13 16:43:12] Run complete: 1 days 02:52:56 elapsed