[2019-07-05 10:57:35] Beginning TopHat run (v2.1.1)
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[2019-07-05 10:57:35] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 10:57:36] Checking for Bowtie index files (genome)..
[2019-07-05 10:57:36] Checking for reference FASTA file
[2019-07-05 10:57:36] Generating SAM header for Bowtie2Index/genome
[2019-07-05 10:57:37] Reading known junctions from GTF file
[2019-07-05 10:57:40] Preparing reads
	 left reads: min. length=150, max. length=150, 23320020 kept reads (1738 discarded)
	right reads: min. length=150, max. length=150, 23304020 kept reads (17738 discarded)
[2019-07-05 11:12:42] Building transcriptome data files /scratch/7534487.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:12:52] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:16:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:37:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:58:02] Resuming TopHat pipeline with unmapped reads
[2019-07-05 11:58:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:05:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:06:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:06:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:07:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:08:31] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:09:20] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:10:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:19:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:20:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:21:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:22:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:23:40] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:24:50] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:25:54] Searching for junctions via segment mapping
[2019-07-05 13:31:52] Retrieving sequences for splices
[2019-07-05 13:33:03] Indexing splices
[2019-07-05 13:34:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:34:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:35:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:36:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:37:01] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:37:43] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:38:21] Joining segment hits
[2019-07-05 13:41:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:42:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:43:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:44:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:45:15] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:46:11] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:47:01] Joining segment hits
[2019-07-05 13:50:02] Reporting output tracks
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[2019-07-05 14:31:40] A summary of the alignment counts can be found in /scratch/7534487.1.p16/tophat2/align_summary.txt
[2019-07-05 14:31:40] Run complete: 03:34:04 elapsed