[2019-09-05 07:57:57] Beginning TopHat run (v2.1.1)
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[2019-09-05 07:57:57] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-05 07:57:58] Checking for Bowtie index files (genome)..
[2019-09-05 07:57:58] Checking for reference FASTA file
[2019-09-05 07:57:58] Generating SAM header for Bowtie2Index/genome
[2019-09-05 07:58:02] Reading known junctions from GTF file
[2019-09-05 07:58:05] Preparing reads
	 left reads: min. length=150, max. length=150, 28395808 kept reads (7 discarded)
	right reads: min. length=150, max. length=150, 28394741 kept reads (1074 discarded)
[2019-09-05 08:19:07] Building transcriptome data files /scratch/9150991.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-05 08:19:17] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-05 08:23:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-05 09:20:40] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-05 10:20:06] Resuming TopHat pipeline with unmapped reads
[2019-09-05 10:20:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-05 11:12:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-05 11:20:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-05 11:27:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-05 11:35:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-05 11:42:48] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-05 11:49:22] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-05 11:53:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-05 12:46:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-05 12:53:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-05 13:00:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-05 13:08:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-05 13:17:04] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-05 13:23:56] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-05 13:28:18] Searching for junctions via segment mapping
[2019-09-05 13:38:56] Retrieving sequences for splices
[2019-09-05 13:39:59] Indexing splices
[2019-09-05 13:40:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-05 13:42:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-05 13:44:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-05 13:46:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-05 13:48:49] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-05 13:51:13] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-05 13:53:15] Joining segment hits
[2019-09-05 13:58:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-05 14:00:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-05 14:02:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-05 14:04:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-05 14:07:15] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-05 14:09:26] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-05 14:11:10] Joining segment hits
[2019-09-05 14:16:55] Reporting output tracks
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[2019-09-05 14:38:37] A summary of the alignment counts can be found in /scratch/9150991.1.linga/tophat2/align_summary.txt
[2019-09-05 14:38:37] Run complete: 06:40:39 elapsed