[2018-10-12 21:01:13] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:01:13] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:01:14] Checking for Bowtie index files (genome)..
[2018-10-12 21:01:14] Checking for reference FASTA file
[2018-10-12 21:01:14] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:01:19] Reading known junctions from GTF file
[2018-10-12 21:01:23] Preparing reads
	 left reads: min. length=100, max. length=100, 312453 kept reads (271 discarded)
	right reads: min. length=100, max. length=100, 312229 kept reads (495 discarded)
[2018-10-12 21:01:37] Building transcriptome data files /scratch/8792740.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:01:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:09:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:10:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:11:04] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:11:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:11:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:11:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:12:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:12:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:12:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:13:05] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:13:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:13:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:13:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:13:52] Searching for junctions via segment mapping
[2018-10-12 21:16:37] Retrieving sequences for splices
[2018-10-12 21:18:45] Indexing splices
[2018-10-12 21:19:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:19:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:19:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:19:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:19:27] Joining segment hits
[2018-10-12 21:21:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:21:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:22:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:22:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:22:12] Joining segment hits
[2018-10-12 21:24:37] Reporting output tracks
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[2018-10-12 21:27:38] A summary of the alignment counts can be found in /scratch/8792740.1.linga/tophat2/align_summary.txt
[2018-10-12 21:27:38] Run complete: 00:26:24 elapsed