[2018-10-12 22:52:30] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:52:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:52:30] Checking for Bowtie index files (genome)..
[2018-10-12 22:52:30] Checking for reference FASTA file
[2018-10-12 22:52:30] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:52:34] Reading known junctions from GTF file
[2018-10-12 22:52:38] Preparing reads
	 left reads: min. length=100, max. length=100, 154784 kept reads (110 discarded)
	right reads: min. length=100, max. length=100, 154629 kept reads (265 discarded)
[2018-10-12 22:52:45] Building transcriptome data files /scratch/8792813.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:53:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:01:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:01:26] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:01:46] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:01:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:02:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:02:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:02:25] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:02:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:02:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:03:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:03:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:03:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:03:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:03:39] Searching for junctions via segment mapping
[2018-10-12 23:06:02] Retrieving sequences for splices
[2018-10-12 23:08:12] Indexing splices
[2018-10-12 23:08:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:08:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:08:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:08:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:08:48] Joining segment hits
[2018-10-12 23:11:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:11:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:11:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:11:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:11:25] Joining segment hits
[2018-10-12 23:13:39] Reporting output tracks
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[2018-10-12 23:16:41] A summary of the alignment counts can be found in /scratch/8792813.1.linga/tophat2/align_summary.txt
[2018-10-12 23:16:41] Run complete: 00:24:11 elapsed