[2019-07-05 10:57:11] Beginning TopHat run (v2.1.1)
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[2019-07-05 10:57:11] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 10:57:11] Checking for Bowtie index files (genome)..
[2019-07-05 10:57:11] Checking for reference FASTA file
[2019-07-05 10:57:11] Generating SAM header for Bowtie2Index/genome
[2019-07-05 10:57:13] Reading known junctions from GTF file
[2019-07-05 10:57:15] Preparing reads
	 left reads: min. length=150, max. length=150, 21872689 kept reads (1656 discarded)
	right reads: min. length=150, max. length=150, 21859466 kept reads (14879 discarded)
[2019-07-05 11:11:38] Building transcriptome data files /scratch/7534486.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:11:47] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:15:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:31:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:46:36] Resuming TopHat pipeline with unmapped reads
[2019-07-05 11:46:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 11:53:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 11:53:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 11:54:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 11:55:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 11:55:58] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 11:56:37] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 11:57:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:05:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:06:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:07:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:08:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:09:50] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:10:51] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:11:47] Searching for junctions via segment mapping
[2019-07-05 12:54:09] Retrieving sequences for splices
[2019-07-05 12:55:19] Indexing splices
[2019-07-05 12:56:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 12:56:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 12:56:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 12:57:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 12:57:55] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 12:58:22] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 12:58:47] Joining segment hits
[2019-07-05 13:01:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:01:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:02:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:03:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:04:12] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:04:52] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:05:30] Joining segment hits
[2019-07-05 13:08:15] Reporting output tracks
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[2019-07-05 13:42:18] A summary of the alignment counts can be found in /scratch/7534486.1.p16/tophat2/align_summary.txt
[2019-07-05 13:42:18] Run complete: 02:45:07 elapsed