[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 13:43:44] Reading known junctions from GTF file
[2019-07-12 13:43:48] Preparing reads
	 left reads: min. length=151, max. length=151, 64025140 kept reads (4283 discarded)
	right reads: min. length=151, max. length=151, 64014581 kept reads (14842 discarded)
[2019-07-12 15:01:39] Building transcriptome data files /scratch/7678198.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:01:57] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:08:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:55:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:53:23] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:53:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:21:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:58:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:35:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:18:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 22:00:22] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:34:44] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 22:58:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:36:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 03:23:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 04:09:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 04:57:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 05:42:39] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 06:18:47] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 06:44:33] Searching for junctions via segment mapping
[2019-07-13 23:04:02] Retrieving sequences for splices
[2019-07-13 23:06:22] Indexing splices
[2019-07-13 23:07:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 23:56:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 00:32:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 01:04:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 01:37:34] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 02:03:26] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 02:15:20] Joining segment hits
[2019-07-14 03:03:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-14 03:38:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 04:13:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-14 04:47:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-14 05:21:33] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-14 05:48:28] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-14 06:02:16] Joining segment hits
[2019-07-14 06:52:55] Reporting output tracks
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[2019-07-14 09:00:23] A summary of the alignment counts can be found in /scratch/7678198.1.linga/tophat2/align_summary.txt
[2019-07-14 09:00:23] Run complete: 1 days 19:16:45 elapsed