[2019-06-25 02:49:25] Beginning TopHat run (v2.1.1)
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[2019-06-25 02:49:25] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-25 02:49:26] Checking for Bowtie index files (genome)..
[2019-06-25 02:49:26] Checking for reference FASTA file
[2019-06-25 02:49:26] Generating SAM header for Bowtie2Index/genome
[2019-06-25 02:49:28] Reading known junctions from GTF file
[2019-06-25 02:49:32] Preparing reads
	 left reads: min. length=150, max. length=150, 63810604 kept reads (5738 discarded)
	right reads: min. length=150, max. length=150, 63800468 kept reads (15874 discarded)
[2019-06-25 03:50:37] Building transcriptome data files /scratch/7056840.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-25 03:50:53] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-25 03:56:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 04:33:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 05:13:10] Resuming TopHat pipeline with unmapped reads
[2019-06-25 05:13:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 07:04:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 07:20:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 07:37:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 07:53:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 08:08:34] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 08:19:19] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 08:24:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 09:57:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 10:13:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 10:29:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 10:46:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 11:02:16] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 11:14:04] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 11:22:07] Searching for junctions via segment mapping
[2019-06-25 22:09:16] Retrieving sequences for splices
[2019-06-25 22:11:46] Indexing splices
[2019-06-25 22:13:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-25 22:24:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-25 22:36:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-25 22:48:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-25 23:01:13] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-25 23:09:48] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-25 23:12:05] Joining segment hits
[2019-06-25 23:34:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-25 23:47:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 00:00:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 00:14:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 00:27:59] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 00:37:18] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 00:39:47] Joining segment hits
[2019-06-26 01:03:24] Reporting output tracks
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[2019-06-26 03:30:31] A summary of the alignment counts can be found in /scratch/7056840.1.linga/tophat2/align_summary.txt
[2019-06-26 03:30:31] Run complete: 1 days 00:41:06 elapsed