[2019-04-29 17:43:04] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:43:04] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:43:04] Checking for Bowtie index files (genome)..
[2019-04-29 17:43:04] Checking for reference FASTA file
[2019-04-29 17:43:04] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:43:06] Reading known junctions from GTF file
[2019-04-29 17:43:09] Preparing reads
	 left reads: min. length=50, max. length=50, 84668143 kept reads (36519 discarded)
	right reads: min. length=50, max. length=50, 84578571 kept reads (126091 discarded)
[2019-04-29 18:07:07] Building transcriptome data files /scratch/5765375.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 18:07:16] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 18:12:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:26:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:41:21] Resuming TopHat pipeline with unmapped reads
[2019-04-29 18:41:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 19:02:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 19:05:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 19:08:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 19:30:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 19:35:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 19:41:28] Searching for junctions via segment mapping
[2019-04-29 19:47:49] Retrieving sequences for splices
[2019-04-29 19:48:49] Indexing splices
[2019-04-29 19:49:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 19:50:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 19:51:20] Joining segment hits
[2019-04-29 19:52:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 19:54:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 19:55:35] Joining segment hits
[2019-04-29 19:57:29] Reporting output tracks
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[2019-04-29 20:28:34] A summary of the alignment counts can be found in /scratch/5765375.1.p16/tophat2/align_summary.txt
[2019-04-29 20:28:34] Run complete: 02:45:29 elapsed