[2019-06-24 17:59:31] Beginning TopHat run (v2.1.1)
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[2019-06-24 17:59:31] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:59:32] Checking for Bowtie index files (genome)..
[2019-06-24 17:59:32] Checking for reference FASTA file
[2019-06-24 17:59:32] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:59:33] Reading known junctions from GTF file
[2019-06-24 17:59:39] Preparing reads
	 left reads: min. length=101, max. length=101, 49171401 kept reads (758 discarded)
	right reads: min. length=101, max. length=101, 49129585 kept reads (42574 discarded)
[2019-06-24 18:28:27] Building transcriptome data files /scratch/7056786.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:28:36] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:32:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 18:55:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:19:09] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:19:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:32:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 19:34:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 19:35:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 19:37:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 19:39:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:53:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 19:55:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 19:57:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 19:59:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:01:25] Searching for junctions via segment mapping
[2019-06-24 20:21:22] Retrieving sequences for splices
[2019-06-24 20:22:32] Indexing splices
[2019-06-24 20:23:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 20:24:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 20:25:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 20:26:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 20:27:05] Joining segment hits
[2019-06-24 20:29:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 20:31:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 20:32:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 20:33:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 20:34:15] Joining segment hits
[2019-06-24 20:37:08] Reporting output tracks
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[2019-06-24 21:40:57] A summary of the alignment counts can be found in /scratch/7056786.1.p16/tophat2/align_summary.txt
[2019-06-24 21:40:57] Run complete: 03:41:25 elapsed