[2018-10-13 07:57:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:57:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:57:05] Checking for Bowtie index files (genome)..
[2018-10-13 07:57:05] Checking for reference FASTA file
[2018-10-13 07:57:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:57:09] Reading known junctions from GTF file
[2018-10-13 07:57:14] Preparing reads
	 left reads: min. length=100, max. length=100, 960866 kept reads (174 discarded)
	right reads: min. length=100, max. length=100, 960570 kept reads (470 discarded)
[2018-10-13 07:57:54] Building transcriptome data files /scratch/8793100.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:58:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:06:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:07:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:09:00] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:09:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:09:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:09:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:10:16] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:10:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:10:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:11:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:11:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:12:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:12:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:12:28] Searching for junctions via segment mapping
[2018-10-13 08:20:00] Retrieving sequences for splices
[2018-10-13 08:22:09] Indexing splices
[2018-10-13 08:22:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:22:45] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:22:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:23:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:23:14] Joining segment hits
[2018-10-13 08:26:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:26:38] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:26:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:27:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:27:12] Joining segment hits
[2018-10-13 08:30:00] Reporting output tracks
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[2018-10-13 08:48:30] A summary of the alignment counts can be found in /scratch/8793100.1.linga/tophat2/align_summary.txt
[2018-10-13 08:48:30] Run complete: 00:51:25 elapsed