[2018-10-13 15:51:27] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:51:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:51:28] Checking for Bowtie index files (genome)..
[2018-10-13 15:51:28] Checking for reference FASTA file
[2018-10-13 15:51:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:51:30] Reading known junctions from GTF file
[2018-10-13 15:51:32] Preparing reads
	 left reads: min. length=100, max. length=100, 414669 kept reads (131 discarded)
	right reads: min. length=100, max. length=100, 414362 kept reads (438 discarded)
[2018-10-13 15:51:44] Building transcriptome data files /scratch/8793331.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:51:54] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:56:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:56:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:57:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:57:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:57:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:57:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:57:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:57:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:57:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:57:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:58:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:58:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:58:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:58:14] Searching for junctions via segment mapping
[2018-10-13 15:59:49] Retrieving sequences for splices
[2018-10-13 16:00:56] Indexing splices
[2018-10-13 16:01:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:01:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:01:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:01:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:01:16] Joining segment hits
[2018-10-13 16:02:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:02:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:02:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:02:38] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:02:40] Joining segment hits
[2018-10-13 16:03:54] Reporting output tracks
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[2018-10-13 16:06:32] A summary of the alignment counts can be found in /scratch/8793331.1.p8/tophat2/align_summary.txt
[2018-10-13 16:06:32] Run complete: 00:15:04 elapsed