[2019-09-04 11:19:02] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:19:02] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:19:03] Checking for Bowtie index files (genome)..
[2019-09-04 11:19:03] Checking for reference FASTA file
[2019-09-04 11:19:03] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:19:06] Reading known junctions from GTF file
[2019-09-04 11:19:09] Preparing reads
	 left reads: min. length=150, max. length=150, 39308653 kept reads (15 discarded)
	right reads: min. length=150, max. length=150, 39307185 kept reads (1483 discarded)
[2019-09-04 11:46:47] Building transcriptome data files /scratch/9142552.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:47:01] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:51:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:16:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:40:37] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:40:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:23:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:28:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 13:34:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 13:39:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 13:45:36] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:50:30] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:53:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:37:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 14:42:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:48:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:55:06] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:01:20] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:06:59] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:10:34] Searching for junctions via segment mapping
[2019-09-04 15:22:52] Retrieving sequences for splices
[2019-09-04 15:23:55] Indexing splices
[2019-09-04 15:24:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 15:25:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 15:26:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 15:27:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 15:29:05] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 15:30:09] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 15:30:59] Joining segment hits
[2019-09-04 15:35:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 15:36:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 15:37:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 15:39:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 15:40:18] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 15:41:29] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 15:42:28] Joining segment hits
[2019-09-04 15:46:54] Reporting output tracks
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[2019-09-04 16:18:01] A summary of the alignment counts can be found in /scratch/9142552.1.linga/tophat2/align_summary.txt
[2019-09-04 16:18:01] Run complete: 04:58:59 elapsed