[2019-07-03 16:59:35] Beginning TopHat run (v2.1.1)
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[2019-07-03 16:59:35] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-03 16:59:35] Checking for Bowtie index files (genome)..
[2019-07-03 16:59:35] Checking for reference FASTA file
[2019-07-03 16:59:35] Generating SAM header for Bowtie2Index/genome
[2019-07-03 16:59:38] Reading known junctions from GTF file
[2019-07-03 16:59:42] Preparing reads
	 left reads: min. length=150, max. length=150, 31355843 kept reads (454 discarded)
	right reads: min. length=150, max. length=150, 31356221 kept reads (76 discarded)
[2019-07-03 17:35:02] Building transcriptome data files /scratch/7505693.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-03 17:35:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-03 17:42:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:00:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-03 18:20:10] Resuming TopHat pipeline with unmapped reads
[2019-07-03 18:20:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 19:33:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 19:42:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 19:52:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 20:01:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 20:10:08] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 20:15:58] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 20:19:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-03 21:34:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-03 21:45:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-03 21:55:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-03 22:06:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-03 22:16:29] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-03 22:24:03] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-03 22:28:10] Searching for junctions via segment mapping
[2019-07-04 05:09:22] Retrieving sequences for splices
[2019-07-04 05:11:48] Indexing splices
[2019-07-04 05:13:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 05:20:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 05:27:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 05:34:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 05:41:43] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 05:46:20] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 05:47:35] Joining segment hits
[2019-07-04 06:02:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 06:10:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 06:18:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 06:25:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 06:32:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 06:37:36] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 06:38:55] Joining segment hits
[2019-07-04 06:53:48] Reporting output tracks
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[2019-07-04 07:58:11] A summary of the alignment counts can be found in /scratch/7505693.1.linga/tophat2/align_summary.txt
[2019-07-04 07:58:11] Run complete: 14:58:35 elapsed