[2019-07-12 13:43:37] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:43:37] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:43:38] Checking for Bowtie index files (genome)..
[2019-07-12 13:43:38] Checking for reference FASTA file
[2019-07-12 13:43:38] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:43:43] Reading known junctions from GTF file
[2019-07-12 13:43:47] Preparing reads
	 left reads: min. length=151, max. length=151, 60674055 kept reads (3938 discarded)
	right reads: min. length=151, max. length=151, 60664288 kept reads (13705 discarded)
[2019-07-12 14:58:35] Building transcriptome data files /scratch/7678199.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:58:54] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:05:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:43:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:29:56] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:29:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 18:59:05] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:32:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:06:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 20:40:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:19:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 21:50:53] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 22:14:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 01:46:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:23:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:04:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 03:48:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:28:22] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:03:36] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:31:37] Searching for junctions via segment mapping
[2019-07-13 10:55:26] Retrieving sequences for splices
[2019-07-13 10:57:47] Indexing splices
[2019-07-13 10:58:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 11:34:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 12:07:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 12:39:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 13:11:38] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 13:39:07] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 13:54:53] Joining segment hits
[2019-07-13 14:50:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 15:26:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 16:01:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 16:36:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 17:12:21] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 17:40:56] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 17:59:16] Joining segment hits
[2019-07-13 19:01:40] Reporting output tracks
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[2019-07-13 20:47:27] A summary of the alignment counts can be found in /scratch/7678199.1.linga/tophat2/align_summary.txt
[2019-07-13 20:47:27] Run complete: 1 days 07:03:50 elapsed