[2019-06-25 02:34:05] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-25 02:34:05] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-25 02:34:05] Checking for Bowtie index files (genome)..
[2019-06-25 02:34:05] Checking for reference FASTA file
[2019-06-25 02:34:05] Generating SAM header for Bowtie2Index/genome
[2019-06-25 02:34:07] Reading known junctions from GTF file
[2019-06-25 02:34:11] Preparing reads
	 left reads: min. length=150, max. length=150, 62881296 kept reads (5644 discarded)
	right reads: min. length=150, max. length=150, 62871522 kept reads (15418 discarded)
[2019-06-25 03:42:01] Building transcriptome data files /scratch/7056838.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-25 03:42:17] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-25 03:48:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 04:30:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 05:15:41] Resuming TopHat pipeline with unmapped reads
[2019-06-25 05:15:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 06:35:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 06:49:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 07:05:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 07:21:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 07:36:17] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 07:47:35] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 07:52:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 09:15:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 09:32:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 09:49:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 10:07:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 10:24:41] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 10:37:46] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 10:45:05] Searching for junctions via segment mapping
[2019-06-26 00:18:41] Retrieving sequences for splices
[2019-06-26 00:21:12] Indexing splices
[2019-06-26 00:22:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-26 00:36:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 00:53:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 01:10:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 01:26:37] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 01:38:13] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 01:41:13] Joining segment hits
[2019-06-26 02:10:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-26 02:26:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 02:41:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 02:55:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 03:09:47] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 03:19:45] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 03:25:02] Joining segment hits
[2019-06-26 03:54:39] Reporting output tracks
-----------------------------------------------
[2019-06-26 06:14:45] A summary of the alignment counts can be found in /scratch/7056838.1.linga/tophat2/align_summary.txt
[2019-06-26 06:14:45] Run complete: 1 days 03:40:40 elapsed