[2019-04-30 23:48:48] Beginning TopHat run (v2.1.1)
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[2019-04-30 23:48:48] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-30 23:48:48] Checking for Bowtie index files (genome)..
[2019-04-30 23:48:48] Checking for reference FASTA file
[2019-04-30 23:48:48] Generating SAM header for Bowtie2Index/genome
[2019-04-30 23:48:50] Reading known junctions from GTF file
[2019-04-30 23:48:52] Preparing reads
	 left reads: min. length=76, max. length=76, 26478142 kept reads (6619 discarded)
	right reads: min. length=76, max. length=76, 26468547 kept reads (16214 discarded)
[2019-04-30 23:59:19] Building transcriptome data files /scratch/5785980.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-04-30 23:59:28] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-01 00:04:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:13:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-01 00:22:58] Resuming TopHat pipeline with unmapped reads
[2019-05-01 00:22:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:25:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:26:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:26:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:27:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-01 00:30:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-05-01 00:30:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-05-01 00:31:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-05-01 00:32:05] Searching for junctions via segment mapping
[2019-05-01 00:38:01] Retrieving sequences for splices
[2019-05-01 00:39:01] Indexing splices
[2019-05-01 00:39:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 00:39:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 00:39:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 00:40:02] Joining segment hits
[2019-05-01 00:41:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-05-01 00:41:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-05-01 00:41:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-05-01 00:42:10] Joining segment hits
[2019-05-01 00:43:33] Reporting output tracks
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[2019-05-01 01:07:31] A summary of the alignment counts can be found in /scratch/5785980.1.p8/tophat2/align_summary.txt
[2019-05-01 01:07:31] Run complete: 01:18:42 elapsed