[2019-06-19 17:27:05] Beginning TopHat run (v2.1.1)
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[2019-06-19 17:27:05] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-19 17:27:05] Checking for Bowtie index files (genome)..
[2019-06-19 17:27:05] Checking for reference FASTA file
[2019-06-19 17:27:05] Generating SAM header for Bowtie2Index/genome
[2019-06-19 17:27:07] Reading known junctions from GTF file
[2019-06-19 17:27:09] Preparing reads
	 left reads: min. length=150, max. length=150, 21843261 kept reads (6 discarded)
	right reads: min. length=150, max. length=150, 21840019 kept reads (3248 discarded)
[2019-06-19 17:43:42] Building transcriptome data files /scratch/6873228.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-06-19 17:43:50] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-19 17:48:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-19 18:01:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-19 18:14:34] Resuming TopHat pipeline with unmapped reads
[2019-06-19 18:14:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-19 18:26:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-19 18:28:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-19 18:30:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-19 18:32:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-19 18:34:03] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-19 18:35:31] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-19 18:36:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-19 18:51:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-19 18:53:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-19 18:56:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-19 18:58:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-19 19:01:15] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-19 19:03:26] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-19 19:05:03] Searching for junctions via segment mapping
[2019-06-19 19:57:13] Retrieving sequences for splices
[2019-06-19 19:58:23] Indexing splices
[2019-06-19 19:58:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-19 19:59:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-19 20:00:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-19 20:01:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-19 20:02:05] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-19 20:02:45] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-19 20:03:03] Joining segment hits
[2019-06-19 20:05:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-19 20:07:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-19 20:08:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-19 20:09:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-19 20:10:10] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-19 20:10:58] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-19 20:11:25] Joining segment hits
[2019-06-19 20:14:27] Reporting output tracks
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[2019-06-19 20:40:20] A summary of the alignment counts can be found in /scratch/6873228.1.p/tophat2/align_summary.txt
[2019-06-19 20:40:20] Run complete: 03:13:14 elapsed