[2019-07-03 17:15:18] Beginning TopHat run (v2.1.1)
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[2019-07-03 17:15:18] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 17:15:37] Checking for Bowtie index files (genome)..
[2019-07-03 17:15:37] Checking for reference FASTA file
[2019-07-03 17:15:37] Generating SAM header for Bowtie2Index/genome
[2019-07-03 17:15:42] Reading known junctions from GTF file
[2019-07-03 17:15:45] Preparing reads
	 left reads: min. length=150, max. length=150, 31425880 kept reads (399 discarded)
	right reads: min. length=150, max. length=150, 31426211 kept reads (68 discarded)
[2019-07-03 17:39:30] Building transcriptome data files /scratch/7505694.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 17:39:39] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 17:43:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 17:57:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:12:30] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:12:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 18:41:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 18:46:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 18:52:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 18:58:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 19:04:34] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 19:08:24] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 19:10:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:36:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:43:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 19:53:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:00:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:09:01] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:15:09] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:18:12] Searching for junctions via segment mapping
[2019-07-04 02:39:11] Retrieving sequences for splices
[2019-07-04 02:40:17] Indexing splices
[2019-07-04 02:40:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 02:47:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 02:53:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 03:00:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 03:06:16] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 03:10:11] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 03:11:07] Joining segment hits
[2019-07-04 03:19:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 03:26:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 03:33:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 03:39:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 03:46:06] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 03:49:54] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 03:50:54] Joining segment hits
[2019-07-04 04:00:03] Reporting output tracks
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[2019-07-04 04:41:03] A summary of the alignment counts can be found in /scratch/7505694.1.linga/tophat2/align_summary.txt
[2019-07-04 04:41:03] Run complete: 11:25:44 elapsed