[2018-10-13 05:43:39] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 05:43:39] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:43:39] Checking for Bowtie index files (genome)..
[2018-10-13 05:43:39] Checking for reference FASTA file
[2018-10-13 05:43:39] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:43:41] Reading known junctions from GTF file
[2018-10-13 05:43:43] Preparing reads
	 left reads: min. length=100, max. length=100, 779240 kept reads (158 discarded)
	right reads: min. length=100, max. length=100, 778974 kept reads (424 discarded)
[2018-10-13 05:44:06] Building transcriptome data files /scratch/8793033.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:44:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:49:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:50:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:50:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:50:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:51:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:51:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:51:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:51:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:51:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:52:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:52:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:52:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:52:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:52:26] Searching for junctions via segment mapping
[2018-10-13 05:55:33] Retrieving sequences for splices
[2018-10-13 05:56:45] Indexing splices
[2018-10-13 05:56:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:57:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:57:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:57:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:57:13] Joining segment hits
[2018-10-13 05:58:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:58:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:58:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:58:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:58:50] Joining segment hits
[2018-10-13 06:00:12] Reporting output tracks
-----------------------------------------------
[2018-10-13 06:08:44] A summary of the alignment counts can be found in /scratch/8793033.1.c/tophat2/align_summary.txt
[2018-10-13 06:08:44] Run complete: 00:25:04 elapsed