[2019-07-03 23:54:32] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-03 23:54:32] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 23:54:32] Checking for Bowtie index files (genome)..
[2019-07-03 23:54:32] Checking for reference FASTA file
[2019-07-03 23:54:32] Generating SAM header for Bowtie2Index/genome
[2019-07-03 23:54:34] Reading known junctions from GTF file
[2019-07-03 23:54:36] Preparing reads
	 left reads: min. length=150, max. length=150, 33119323 kept reads (444 discarded)
	right reads: min. length=150, max. length=150, 33119694 kept reads (73 discarded)
[2019-07-04 00:15:21] Building transcriptome data files /scratch/7505711.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-07-04 00:15:30] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-04 00:19:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 00:36:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 00:52:56] Resuming TopHat pipeline with unmapped reads
[2019-07-04 00:52:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 01:22:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 01:28:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 01:34:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 01:40:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 01:45:52] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 01:49:57] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 01:52:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 02:24:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 02:30:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 02:36:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 02:42:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 02:48:46] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 02:53:25] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 02:56:17] Searching for junctions via segment mapping
[2019-07-04 06:44:30] Retrieving sequences for splices
[2019-07-04 06:45:42] Indexing splices
[2019-07-04 06:46:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 06:50:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 06:54:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 06:58:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 07:02:02] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 07:04:44] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 07:05:42] Joining segment hits
[2019-07-04 07:12:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 07:16:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 07:20:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 07:25:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 07:28:54] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 07:31:33] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 07:32:37] Joining segment hits
[2019-07-04 07:39:27] Reporting output tracks
-----------------------------------------------
[2019-07-04 08:12:14] A summary of the alignment counts can be found in /scratch/7505711.1.p8/tophat2/align_summary.txt
[2019-07-04 08:12:14] Run complete: 08:17:42 elapsed