[2019-04-29 17:29:46] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:29:46] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:29:48] Checking for Bowtie index files (genome)..
[2019-04-29 17:29:48] Checking for reference FASTA file
[2019-04-29 17:29:48] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:29:49] Reading known junctions from GTF file
[2019-04-29 17:29:52] Preparing reads
	 left reads: min. length=50, max. length=50, 127137991 kept reads (28243 discarded)
	right reads: min. length=50, max. length=50, 127112117 kept reads (54117 discarded)
[2019-04-29 18:09:14] Building transcriptome data files /scratch/5765362.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 18:09:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 18:14:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:49:04] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 19:24:00] Resuming TopHat pipeline with unmapped reads
[2019-04-29 19:24:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 19:34:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 19:36:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 19:38:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 19:50:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 19:53:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 19:56:38] Searching for junctions via segment mapping
[2019-04-29 20:03:59] Retrieving sequences for splices
[2019-04-29 20:04:59] Indexing splices
[2019-04-29 20:05:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 20:05:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 20:06:06] Joining segment hits
[2019-04-29 20:07:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 20:08:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 20:08:44] Joining segment hits
[2019-04-29 20:10:18] Reporting output tracks
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[2019-04-29 22:15:04] A summary of the alignment counts can be found in /scratch/5765362.1.p/tophat2/align_summary.txt
[2019-04-29 22:15:04] Run complete: 04:45:17 elapsed