[2019-09-04 11:22:35] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:22:35] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:22:35] Checking for Bowtie index files (genome)..
[2019-09-04 11:22:35] Checking for reference FASTA file
[2019-09-04 11:22:35] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:22:40] Reading known junctions from GTF file
[2019-09-04 11:22:43] Preparing reads
	 left reads: min. length=150, max. length=150, 33537644 kept reads (15 discarded)
	right reads: min. length=150, max. length=150, 33536420 kept reads (1239 discarded)
[2019-09-04 11:54:15] Building transcriptome data files /scratch/9142567.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:54:31] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 12:03:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:27:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 14:41:55] Resuming TopHat pipeline with unmapped reads
[2019-09-04 14:41:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 16:16:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 16:30:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 16:43:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 16:58:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 17:11:57] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 17:23:32] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 17:29:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 19:03:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 19:16:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 19:28:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 19:42:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 19:54:53] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 20:06:10] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 20:12:07] Searching for junctions via segment mapping
[2019-09-04 20:36:00] Retrieving sequences for splices
[2019-09-04 20:38:15] Indexing splices
[2019-09-04 20:40:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 20:44:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 20:48:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 20:52:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 20:56:51] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 21:00:10] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 21:02:17] Joining segment hits
[2019-09-04 21:14:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 21:17:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 21:19:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 21:22:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 21:25:49] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 21:28:40] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 21:30:54] Joining segment hits
[2019-09-04 21:42:14] Reporting output tracks
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[2019-09-04 22:38:53] A summary of the alignment counts can be found in /scratch/9142567.1.linga/tophat2/align_summary.txt
[2019-09-04 22:38:53] Run complete: 11:16:17 elapsed