[2019-07-04 02:29:48] Beginning TopHat run (v2.1.1)
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[2019-07-04 02:29:48] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-04 02:29:49] Checking for Bowtie index files (genome)..
[2019-07-04 02:29:49] Checking for reference FASTA file
[2019-07-04 02:29:49] Generating SAM header for Bowtie2Index/genome
[2019-07-04 02:29:50] Reading known junctions from GTF file
[2019-07-04 02:29:52] Preparing reads
	 left reads: min. length=150, max. length=150, 34225210 kept reads (464 discarded)
	right reads: min. length=150, max. length=150, 34225591 kept reads (83 discarded)
[2019-07-04 02:50:40] Building transcriptome data files /scratch/7505714.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-07-04 02:50:49] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-04 02:54:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 03:09:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 03:25:01] Resuming TopHat pipeline with unmapped reads
[2019-07-04 03:25:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 03:57:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 04:02:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 04:07:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 04:12:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 04:17:04] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 04:21:02] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 04:23:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 04:56:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 05:02:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 05:07:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 05:12:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 05:18:00] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 05:22:23] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 05:25:12] Searching for junctions via segment mapping
[2019-07-04 07:13:30] Retrieving sequences for splices
[2019-07-04 07:14:41] Indexing splices
[2019-07-04 07:15:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 07:18:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 07:21:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 07:24:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 07:26:56] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 07:28:54] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 07:29:50] Joining segment hits
[2019-07-04 07:34:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 07:38:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 07:41:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 07:44:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 07:47:21] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 07:49:21] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 07:50:20] Joining segment hits
[2019-07-04 07:55:49] Reporting output tracks
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[2019-07-04 08:21:45] A summary of the alignment counts can be found in /scratch/7505714.1.p16/tophat2/align_summary.txt
[2019-07-04 08:21:45] Run complete: 05:51:56 elapsed