[2019-07-17 19:08:44] Beginning TopHat run (v2.1.1)
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[2019-07-17 19:08:44] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-17 19:08:44] Checking for Bowtie index files (genome)..
[2019-07-17 19:08:44] Checking for reference FASTA file
[2019-07-17 19:08:44] Generating SAM header for Bowtie2Index/genome
[2019-07-17 19:08:47] Reading known junctions from GTF file
[2019-07-17 19:08:50] Preparing reads
	 left reads: min. length=150, max. length=150, 69236229 kept reads (6124 discarded)
	right reads: min. length=150, max. length=150, 69225254 kept reads (17099 discarded)
[2019-07-17 20:01:58] Building transcriptome data files /scratch/7775057.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-17 20:02:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-17 20:06:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 20:31:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-17 20:59:05] Resuming TopHat pipeline with unmapped reads
[2019-07-17 20:59:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 21:46:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-17 21:53:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-17 22:02:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-17 22:10:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-17 22:18:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-17 22:24:04] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-17 22:27:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-17 23:16:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-17 23:24:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-17 23:33:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-17 23:42:47] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-17 23:51:28] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-17 23:58:15] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-18 00:02:31] Searching for junctions via segment mapping
[2019-07-18 05:03:44] Retrieving sequences for splices
[2019-07-18 05:04:56] Indexing splices
[2019-07-18 05:06:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 05:11:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 05:16:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 05:22:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 05:27:55] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 05:31:46] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 05:32:56] Joining segment hits
[2019-07-18 05:42:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-18 05:48:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-18 05:54:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-18 05:59:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-18 06:05:01] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-18 06:08:51] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-18 06:10:01] Joining segment hits
[2019-07-18 06:20:10] Reporting output tracks
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[2019-07-18 07:24:05] A summary of the alignment counts can be found in /scratch/7775057.1.linga/tophat2/align_summary.txt
[2019-07-18 07:24:05] Run complete: 12:15:20 elapsed