[2019-07-05 10:58:44] Beginning TopHat run (v2.1.1)
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[2019-07-05 10:58:44] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 10:58:44] Checking for Bowtie index files (genome)..
[2019-07-05 10:58:44] Checking for reference FASTA file
[2019-07-05 10:58:44] Generating SAM header for Bowtie2Index/genome
[2019-07-05 10:58:46] Reading known junctions from GTF file
[2019-07-05 10:58:48] Preparing reads
	 left reads: min. length=150, max. length=150, 20658968 kept reads (1632 discarded)
	right reads: min. length=150, max. length=150, 20646721 kept reads (13879 discarded)
[2019-07-05 11:12:11] Building transcriptome data files /scratch/7534485.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:12:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:16:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:34:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:52:03] Resuming TopHat pipeline with unmapped reads
[2019-07-05 11:52:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 11:58:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 11:58:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 11:59:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:00:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:01:00] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:01:42] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:02:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:10:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:11:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:12:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:14:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:15:02] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:16:03] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:17:00] Searching for junctions via segment mapping
[2019-07-05 13:16:57] Retrieving sequences for splices
[2019-07-05 13:18:07] Indexing splices
[2019-07-05 13:18:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:19:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:20:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:20:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:21:17] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:21:51] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:22:20] Joining segment hits
[2019-07-05 13:24:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:25:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:26:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:27:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:28:34] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:29:23] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:30:07] Joining segment hits
[2019-07-05 13:33:06] Reporting output tracks
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[2019-07-05 14:15:46] A summary of the alignment counts can be found in /scratch/7534485.1.p8/tophat2/align_summary.txt
[2019-07-05 14:15:46] Run complete: 03:17:02 elapsed