[2019-07-12 13:47:21] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:47:21] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:47:22] Checking for Bowtie index files (genome)..
[2019-07-12 13:47:22] Checking for reference FASTA file
[2019-07-12 13:47:22] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:47:24] Reading known junctions from GTF file
[2019-07-12 13:47:27] Preparing reads
	 left reads: min. length=151, max. length=151, 76927118 kept reads (5429 discarded)
	right reads: min. length=151, max. length=151, 76913655 kept reads (18892 discarded)
[2019-07-12 15:11:07] Building transcriptome data files /scratch/7678194.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:11:26] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:18:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 18:42:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 22:10:16] Resuming TopHat pipeline with unmapped reads
[2019-07-12 22:10:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 01:37:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:19:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:04:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 03:55:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:41:29] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:20:49] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:47:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 10:06:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 10:53:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 11:38:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 12:25:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 13:12:23] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 13:53:56] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 14:21:51] Searching for junctions via segment mapping
[2019-07-15 01:03:51] Retrieving sequences for splices
[2019-07-15 01:05:56] Indexing splices
[2019-07-15 01:08:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-15 01:54:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-15 02:39:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-15 03:22:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-15 04:04:18] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-15 04:36:43] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-15 04:50:34] Joining segment hits
[2019-07-15 05:55:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-15 06:42:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-15 07:27:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-15 08:14:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-15 08:57:20] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-15 09:31:41] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-15 09:46:03] Joining segment hits
[2019-07-15 10:54:10] Reporting output tracks
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[2019-07-15 14:10:47] A summary of the alignment counts can be found in /scratch/7678194.1.linga/tophat2/align_summary.txt
[2019-07-15 14:10:47] Run complete: 3 days 00:23:25 elapsed