[2019-07-12 13:50:16] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:50:16] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:50:16] Checking for Bowtie index files (genome)..
[2019-07-12 13:50:16] Checking for reference FASTA file
[2019-07-12 13:50:16] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:50:19] Reading known junctions from GTF file
[2019-07-12 13:50:23] Preparing reads
	 left reads: min. length=151, max. length=151, 58881648 kept reads (98 discarded)
	right reads: min. length=151, max. length=151, 58875493 kept reads (6253 discarded)
[2019-07-12 14:58:33] Building transcriptome data files /scratch/7678203.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 14:58:52] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:05:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 15:41:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 16:24:31] Resuming TopHat pipeline with unmapped reads
[2019-07-12 16:24:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 19:14:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 19:53:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 20:31:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-12 21:13:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-12 21:52:43] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-12 22:20:39] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-12 22:40:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 02:04:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 02:46:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 03:29:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 04:11:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 04:51:11] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 05:22:37] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 05:46:57] Searching for junctions via segment mapping
[2019-07-13 08:54:30] Retrieving sequences for splices
[2019-07-13 08:57:11] Indexing splices
[2019-07-13 08:58:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 09:57:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 10:52:13] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 11:47:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 12:37:58] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 13:15:23] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 13:34:06] Joining segment hits
[2019-07-13 14:44:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-13 15:38:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-13 16:32:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-13 17:24:43] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-13 18:13:22] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-13 18:50:48] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-13 19:11:34] Joining segment hits
[2019-07-13 20:15:06] Reporting output tracks
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[2019-07-13 21:25:18] A summary of the alignment counts can be found in /scratch/7678203.1.linga/tophat2/align_summary.txt
[2019-07-13 21:25:18] Run complete: 1 days 07:35:01 elapsed