[2018-10-13 13:15:42] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 13:15:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:15:42] Checking for Bowtie index files (genome)..
[2018-10-13 13:15:42] Checking for reference FASTA file
[2018-10-13 13:15:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:15:44] Reading known junctions from GTF file
[2018-10-13 13:15:47] Preparing reads
	 left reads: min. length=100, max. length=100, 362882 kept reads (53 discarded)
	right reads: min. length=100, max. length=100, 362796 kept reads (139 discarded)
[2018-10-13 13:15:58] Building transcriptome data files /scratch/8793258.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:16:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:21:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:21:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:21:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:21:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:21:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:22:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:22:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:22:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:22:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:22:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:22:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:22:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:22:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:22:43] Searching for junctions via segment mapping
[2018-10-13 13:25:03] Retrieving sequences for splices
[2018-10-13 13:26:10] Indexing splices
[2018-10-13 13:26:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:26:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:26:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:26:31] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:26:35] Joining segment hits
[2018-10-13 13:27:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:27:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:27:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:27:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:27:59] Joining segment hits
[2018-10-13 13:29:13] Reporting output tracks
-----------------------------------------------
[2018-10-13 13:33:18] A summary of the alignment counts can be found in /scratch/8793258.1.p8/tophat2/align_summary.txt
[2018-10-13 13:33:18] Run complete: 00:17:35 elapsed