[2019-09-04 11:22:11] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:22:11] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:22:11] Checking for Bowtie index files (genome)..
[2019-09-04 11:22:11] Checking for reference FASTA file
[2019-09-04 11:22:11] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:22:15] Reading known junctions from GTF file
[2019-09-04 11:22:19] Preparing reads
	 left reads: min. length=150, max. length=150, 33242878 kept reads (8 discarded)
	right reads: min. length=150, max. length=150, 33241624 kept reads (1262 discarded)
[2019-09-04 11:53:32] Building transcriptome data files /scratch/9142555.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:53:48] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 12:02:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:32:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:03:38] Resuming TopHat pipeline with unmapped reads
[2019-09-04 13:03:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:11:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 14:19:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:28:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:37:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:45:57] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:52:06] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:55:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 16:05:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 16:13:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 16:23:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 16:32:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 16:42:05] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 16:49:48] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 16:54:11] Searching for junctions via segment mapping
[2019-09-04 17:18:33] Retrieving sequences for splices
[2019-09-04 17:20:43] Indexing splices
[2019-09-04 17:22:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:23:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:25:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:27:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:29:41] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:31:24] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:32:36] Joining segment hits
[2019-09-04 17:40:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:42:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:44:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:47:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:49:27] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:51:31] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:52:55] Joining segment hits
[2019-09-04 18:01:22] Reporting output tracks
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[2019-09-04 18:48:02] A summary of the alignment counts can be found in /scratch/9142555.1.linga/tophat2/align_summary.txt
[2019-09-04 18:48:02] Run complete: 07:25:51 elapsed