[2018-10-13 02:46:29] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 02:46:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:46:30] Checking for Bowtie index files (genome)..
[2018-10-13 02:46:30] Checking for reference FASTA file
[2018-10-13 02:46:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:46:32] Reading known junctions from GTF file
[2018-10-13 02:46:34] Preparing reads
	 left reads: min. length=100, max. length=100, 399172 kept reads (245 discarded)
	right reads: min. length=100, max. length=100, 398723 kept reads (694 discarded)
[2018-10-13 02:46:46] Building transcriptome data files /scratch/8792928.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:46:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:52:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:52:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:53:15] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:53:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:53:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:53:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:53:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:53:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:54:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:54:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:54:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:54:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:54:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:54:55] Searching for junctions via segment mapping
[2018-10-13 02:56:22] Retrieving sequences for splices
[2018-10-13 02:57:35] Indexing splices
[2018-10-13 02:57:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:57:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:57:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:57:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:57:56] Joining segment hits
[2018-10-13 02:59:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:59:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:59:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:59:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:59:28] Joining segment hits
[2018-10-13 03:00:50] Reporting output tracks
-----------------------------------------------
[2018-10-13 03:02:49] A summary of the alignment counts can be found in /scratch/8792928.1.c/tophat2/align_summary.txt
[2018-10-13 03:02:49] Run complete: 00:16:19 elapsed