[2019-07-12 13:46:11] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:46:11] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:46:11] Checking for Bowtie index files (genome)..
[2019-07-12 13:46:11] Checking for reference FASTA file
[2019-07-12 13:46:11] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:46:14] Reading known junctions from GTF file
[2019-07-12 13:46:17] Preparing reads
	 left reads: min. length=151, max. length=151, 70293008 kept reads (119 discarded)
	right reads: min. length=151, max. length=151, 70285524 kept reads (7603 discarded)
[2019-07-12 15:10:46] Building transcriptome data files /scratch/7678193.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:11:04] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:18:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:07:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 17:00:50] Resuming TopHat pipeline with unmapped reads
[2019-07-12 17:00:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 20:20:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 20:52:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 21:25:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:59:44] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 22:34:46] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:59:19] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 23:15:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:57:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 03:38:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 04:19:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 04:58:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 05:35:57] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 06:05:44] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 06:27:15] Searching for junctions via segment mapping
[2019-07-13 22:01:46] Retrieving sequences for splices
[2019-07-13 22:04:17] Indexing splices
[2019-07-13 22:06:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 22:53:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 23:51:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 00:33:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 01:06:24] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 01:28:52] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 01:41:14] Joining segment hits
[2019-07-14 02:33:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-14 03:05:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 03:38:04] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 04:12:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 04:42:48] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 05:06:11] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 05:19:11] Joining segment hits
[2019-07-14 06:10:24] Reporting output tracks
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[2019-07-14 08:36:55] A summary of the alignment counts can be found in /scratch/7678193.1.linga/tophat2/align_summary.txt
[2019-07-14 08:36:55] Run complete: 1 days 18:50:44 elapsed