[2019-06-19 17:24:08] Beginning TopHat run (v2.1.1)
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[2019-06-19 17:24:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-19 17:24:08] Checking for Bowtie index files (genome)..
[2019-06-19 17:24:08] Checking for reference FASTA file
[2019-06-19 17:24:08] Generating SAM header for Bowtie2Index/genome
[2019-06-19 17:24:11] Reading known junctions from GTF file
[2019-06-19 17:24:15] Preparing reads
	 left reads: min. length=150, max. length=150, 23525033 kept reads (10 discarded)
	right reads: min. length=150, max. length=150, 23521045 kept reads (3998 discarded)
[2019-06-19 18:04:24] Building transcriptome data files /scratch/6873227.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-19 18:04:43] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-19 18:12:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-19 18:40:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-19 19:11:34] Resuming TopHat pipeline with unmapped reads
[2019-06-19 19:11:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-19 20:17:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-19 20:29:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-19 20:42:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-19 20:53:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-19 21:05:28] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-19 21:14:11] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-19 21:17:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-19 22:08:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-19 22:21:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-19 22:33:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-19 22:46:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-19 23:00:08] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-19 23:10:34] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-19 23:16:31] Searching for junctions via segment mapping
[2019-06-20 06:32:31] Retrieving sequences for splices
[2019-06-20 06:35:02] Indexing splices
[2019-06-20 06:35:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-20 06:45:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-20 06:55:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-20 07:04:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-20 07:14:02] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-20 07:19:36] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-20 07:21:00] Joining segment hits
[2019-06-20 07:39:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-20 07:50:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-20 07:59:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-20 08:10:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-20 08:20:08] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-20 08:26:19] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-20 08:28:28] Joining segment hits
[2019-06-20 08:46:23] Reporting output tracks
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[2019-06-20 09:55:12] A summary of the alignment counts can be found in /scratch/6873227.1.linga/tophat2/align_summary.txt
[2019-06-20 09:55:12] Run complete: 16:31:03 elapsed