[2018-10-12 21:30:58] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:30:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:30:58] Checking for Bowtie index files (genome)..
[2018-10-12 21:30:58] Checking for reference FASTA file
[2018-10-12 21:30:58] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:31:03] Reading known junctions from GTF file
[2018-10-12 21:31:07] Preparing reads
	 left reads: min. length=100, max. length=100, 293525 kept reads (168 discarded)
	right reads: min. length=100, max. length=100, 293274 kept reads (419 discarded)
[2018-10-12 21:31:20] Building transcriptome data files /scratch/8792756.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:31:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:40:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:41:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:41:42] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:41:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:42:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:42:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:42:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:42:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:42:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:43:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:43:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:43:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:44:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:44:19] Searching for junctions via segment mapping
[2018-10-12 21:46:56] Retrieving sequences for splices
[2018-10-12 21:49:11] Indexing splices
[2018-10-12 21:49:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:49:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:49:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:49:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:49:48] Joining segment hits
[2018-10-12 21:52:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:52:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:52:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:52:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:52:39] Joining segment hits
[2018-10-12 21:55:17] Reporting output tracks
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[2018-10-12 21:58:38] A summary of the alignment counts can be found in /scratch/8792756.1.linga/tophat2/align_summary.txt
[2018-10-12 21:58:38] Run complete: 00:27:40 elapsed