[2019-07-05 14:40:57] Beginning TopHat run (v2.1.1)
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[2019-07-05 14:40:57] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 14:40:57] Checking for Bowtie index files (genome)..
[2019-07-05 14:40:57] Checking for reference FASTA file
[2019-07-05 14:40:57] Generating SAM header for Bowtie2Index/genome
[2019-07-05 14:41:00] Reading known junctions from GTF file
[2019-07-05 14:41:03] Preparing reads
	 left reads: min. length=150, max. length=150, 23013512 kept reads (1742 discarded)
	right reads: min. length=150, max. length=150, 22997629 kept reads (17625 discarded)
[2019-07-05 15:03:16] Building transcriptome data files /scratch/7534490.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 15:03:25] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 15:06:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 15:18:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 15:31:01] Resuming TopHat pipeline with unmapped reads
[2019-07-05 15:31:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 15:38:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 15:39:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 15:39:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 15:40:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 15:41:19] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 15:42:01] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 15:42:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 15:52:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 15:53:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 15:54:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 15:55:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 15:56:16] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 15:57:20] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 15:58:19] Searching for junctions via segment mapping
[2019-07-05 16:40:30] Retrieving sequences for splices
[2019-07-05 16:41:35] Indexing splices
[2019-07-05 16:42:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:42:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:43:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:43:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:44:25] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:44:55] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:45:25] Joining segment hits
[2019-07-05 16:47:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:48:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:49:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:49:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:50:42] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:51:23] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:52:00] Joining segment hits
[2019-07-05 16:54:34] Reporting output tracks
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[2019-07-05 17:29:34] A summary of the alignment counts can be found in /scratch/7534490.1.linga/tophat2/align_summary.txt
[2019-07-05 17:29:34] Run complete: 02:48:37 elapsed