[2018-10-13 16:56:27] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 16:56:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:56:27] Checking for Bowtie index files (genome)..
[2018-10-13 16:56:27] Checking for reference FASTA file
[2018-10-13 16:56:27] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:56:29] Reading known junctions from GTF file
[2018-10-13 16:56:31] Preparing reads
	 left reads: min. length=100, max. length=100, 162510 kept reads (146 discarded)
	right reads: min. length=100, max. length=100, 162401 kept reads (255 discarded)
[2018-10-13 16:56:36] Building transcriptome data files /scratch/8793377.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:56:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:01:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:01:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:01:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:01:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:02:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:02:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:02:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:02:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:02:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:02:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:02:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:02:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:02:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:02:45] Searching for junctions via segment mapping
[2018-10-13 17:03:56] Retrieving sequences for splices
[2018-10-13 17:05:03] Indexing splices
[2018-10-13 17:05:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:05:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:05:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:05:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:05:21] Joining segment hits
[2018-10-13 17:06:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:06:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:06:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:06:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:06:38] Joining segment hits
[2018-10-13 17:07:46] Reporting output tracks
-----------------------------------------------
[2018-10-13 17:09:08] A summary of the alignment counts can be found in /scratch/8793377.1.p8/tophat2/align_summary.txt
[2018-10-13 17:09:08] Run complete: 00:12:41 elapsed