[2019-07-12 13:32:01] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:32:01] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:32:01] Checking for Bowtie index files (genome)..
[2019-07-12 13:32:01] Checking for reference FASTA file
[2019-07-12 13:32:01] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:32:07] Reading known junctions from GTF file
[2019-07-12 13:32:11] Preparing reads
	 left reads: min. length=151, max. length=151, 57400737 kept reads (3712 discarded)
	right reads: min. length=151, max. length=151, 57391491 kept reads (12958 discarded)
[2019-07-12 14:41:05] Building transcriptome data files /scratch/7678206.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:41:27] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 14:49:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:28:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:11:07] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:11:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 18:55:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:26:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 19:56:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 20:27:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:00:18] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 21:27:33] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 21:50:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 01:34:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:10:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 02:47:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 03:22:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:04:17] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 04:35:33] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:00:21] Searching for junctions via segment mapping
[2019-07-13 06:21:59] Retrieving sequences for splices
[2019-07-13 06:26:28] Indexing splices
[2019-07-13 06:27:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 06:50:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 07:09:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 07:28:43] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 07:48:05] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 08:04:36] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 08:15:28] Joining segment hits
[2019-07-13 08:55:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 09:16:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 09:36:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 09:56:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 10:16:11] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 10:32:52] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 10:44:36] Joining segment hits
[2019-07-13 11:26:49] Reporting output tracks
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[2019-07-13 12:41:47] A summary of the alignment counts can be found in /scratch/7678206.1.linga/tophat2/align_summary.txt
[2019-07-13 12:41:47] Run complete: 23:09:45 elapsed