[2019-07-17 22:23:31] Beginning TopHat run (v2.1.1)
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[2019-07-17 22:23:31] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 22:23:31] Checking for Bowtie index files (genome)..
[2019-07-17 22:23:31] Checking for reference FASTA file
[2019-07-17 22:23:31] Generating SAM header for Bowtie2Index/genome
[2019-07-17 22:23:35] Reading known junctions from GTF file
[2019-07-17 22:23:38] Preparing reads
	 left reads: min. length=150, max. length=150, 26446286 kept reads (506 discarded)
	right reads: min. length=150, max. length=150, 26446684 kept reads (108 discarded)
[2019-07-17 22:54:42] Building transcriptome data files /scratch/7776703.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 22:55:01] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 23:02:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 23:27:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 23:53:47] Resuming TopHat pipeline with unmapped reads
[2019-07-17 23:53:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 00:29:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 00:36:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 00:44:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 00:53:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 01:01:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 01:07:16] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 01:09:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-18 01:47:16] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-18 01:55:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-18 02:03:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-18 02:12:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-18 02:20:56] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-18 02:27:46] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 02:30:51] Searching for junctions via segment mapping
[2019-07-18 12:48:39] Retrieving sequences for splices
[2019-07-18 12:50:53] Indexing splices
[2019-07-18 12:53:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 13:02:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 13:12:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 13:22:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 13:32:49] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 13:40:16] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 13:42:28] Joining segment hits
[2019-07-18 13:59:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 14:09:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 14:19:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 14:29:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 14:38:38] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 14:45:59] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 14:48:03] Joining segment hits
[2019-07-18 15:05:37] Reporting output tracks
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[2019-07-18 16:45:59] A summary of the alignment counts can be found in /scratch/7776703.1.linga/tophat2/align_summary.txt
[2019-07-18 16:45:59] Run complete: 18:22:28 elapsed