[2019-07-05 11:10:30] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:10:30] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:10:31] Checking for Bowtie index files (genome)..
[2019-07-05 11:10:31] Checking for reference FASTA file
[2019-07-05 11:10:31] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:10:34] Reading known junctions from GTF file
[2019-07-05 11:10:38] Preparing reads
	 left reads: min. length=150, max. length=150, 23261772 kept reads (1785 discarded)
	right reads: min. length=150, max. length=150, 23247826 kept reads (15731 discarded)
[2019-07-05 11:34:47] Building transcriptome data files /scratch/7534481.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:35:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:41:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:04:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:28:40] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:28:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:43:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:44:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:46:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:47:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:48:51] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:50:14] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:51:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:11:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:14:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:16:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:18:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:20:51] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:22:51] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:24:55] Searching for junctions via segment mapping
[2019-07-05 15:19:19] Retrieving sequences for splices
[2019-07-05 15:21:32] Indexing splices
[2019-07-05 15:23:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:24:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:25:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:26:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:27:51] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:29:21] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:30:38] Joining segment hits
[2019-07-05 15:36:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:38:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:40:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:42:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:44:04] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:45:43] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:47:14] Joining segment hits
[2019-07-05 15:54:11] Reporting output tracks
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[2019-07-05 17:24:18] A summary of the alignment counts can be found in /scratch/7534481.1.linga/tophat2/align_summary.txt
[2019-07-05 17:24:18] Run complete: 06:13:47 elapsed