[2019-06-25 02:46:50] Beginning TopHat run (v2.1.1)
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[2019-06-25 02:46:50] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-25 02:46:51] Checking for Bowtie index files (genome)..
[2019-06-25 02:46:51] Checking for reference FASTA file
[2019-06-25 02:46:51] Generating SAM header for Bowtie2Index/genome
[2019-06-25 02:46:54] Reading known junctions from GTF file
[2019-06-25 02:46:57] Preparing reads
	 left reads: min. length=150, max. length=150, 63997098 kept reads (5841 discarded)
	right reads: min. length=150, max. length=150, 63987140 kept reads (15799 discarded)
[2019-06-25 03:51:14] Building transcriptome data files /scratch/7056839.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-25 03:51:30] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-25 03:57:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 04:37:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-25 05:20:02] Resuming TopHat pipeline with unmapped reads
[2019-06-25 05:20:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 06:42:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 06:57:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 07:14:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 07:29:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 07:45:29] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 07:57:09] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 08:02:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-25 09:23:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-25 09:40:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-25 09:57:54] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-25 10:15:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-25 10:32:54] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-25 10:46:11] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-25 10:53:31] Searching for junctions via segment mapping
[2019-06-26 03:56:16] Retrieving sequences for splices
[2019-06-26 03:59:12] Indexing splices
[2019-06-26 04:00:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-26 04:17:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 04:35:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 04:54:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 05:12:30] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 05:24:00] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 05:26:52] Joining segment hits
[2019-06-26 05:55:55] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-26 06:14:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-26 06:33:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-26 06:50:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-26 07:09:35] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-26 07:21:35] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-26 07:24:32] Joining segment hits
[2019-06-26 07:54:14] Reporting output tracks
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[2019-06-26 10:33:00] A summary of the alignment counts can be found in /scratch/7056839.1.linga/tophat2/align_summary.txt
[2019-06-26 10:33:00] Run complete: 1 days 07:46:10 elapsed