[2018-10-13 02:19:43] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 02:19:43] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:19:44] Checking for Bowtie index files (genome)..
[2018-10-13 02:19:44] Checking for reference FASTA file
[2018-10-13 02:19:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:19:46] Reading known junctions from GTF file
[2018-10-13 02:19:48] Preparing reads
	 left reads: min. length=100, max. length=100, 176860 kept reads (193 discarded)
	right reads: min. length=100, max. length=100, 176695 kept reads (358 discarded)
[2018-10-13 02:19:53] Building transcriptome data files /scratch/8792913.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:20:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:24:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:25:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:25:14] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:25:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:25:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:25:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:25:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:25:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:25:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:26:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:26:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:26:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:26:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:26:20] Searching for junctions via segment mapping
[2018-10-13 02:27:31] Retrieving sequences for splices
[2018-10-13 02:28:38] Indexing splices
[2018-10-13 02:28:48] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:28:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:28:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:28:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:28:57] Joining segment hits
[2018-10-13 02:30:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:30:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:30:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:30:12] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:30:14] Joining segment hits
[2018-10-13 02:31:23] Reporting output tracks
-----------------------------------------------
[2018-10-13 02:32:43] A summary of the alignment counts can be found in /scratch/8792913.1.p16/tophat2/align_summary.txt
[2018-10-13 02:32:43] Run complete: 00:12:59 elapsed