[2019-07-12 13:49:23] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:49:23] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:49:24] Checking for Bowtie index files (genome)..
[2019-07-12 13:49:24] Checking for reference FASTA file
[2019-07-12 13:49:24] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:49:32] Reading known junctions from GTF file
[2019-07-12 13:49:39] Preparing reads
	 left reads: min. length=151, max. length=151, 65267042 kept reads (143 discarded)
	right reads: min. length=151, max. length=151, 65260222 kept reads (6963 discarded)
[2019-07-12 15:39:56] Building transcriptome data files /scratch/7678197.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:40:15] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:49:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 17:21:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 19:05:36] Resuming TopHat pipeline with unmapped reads
[2019-07-12 19:05:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 22:32:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 23:27:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 00:22:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 01:10:18] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 01:50:47] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 02:22:34] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 02:42:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 07:20:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 08:16:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 09:17:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 10:19:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 11:15:25] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 12:04:41] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 12:42:12] Searching for junctions via segment mapping
[2019-07-14 21:07:35] Retrieving sequences for splices
[2019-07-14 21:12:13] Indexing splices
[2019-07-14 21:17:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-14 22:14:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-14 23:12:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-15 00:08:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-15 01:02:43] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-15 01:40:55] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-15 01:56:45] Joining segment hits
[2019-07-15 03:08:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-15 04:08:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-15 05:10:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-15 06:10:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-15 07:06:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-15 07:48:38] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-15 08:09:22] Joining segment hits
[2019-07-15 09:40:42] Reporting output tracks
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[2019-07-15 15:55:58] A summary of the alignment counts can be found in /scratch/7678197.1.linga/tophat2/align_summary.txt
[2019-07-15 15:55:58] Run complete: 3 days 02:06:35 elapsed