[2018-10-13 17:26:11] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:26:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:26:11] Checking for Bowtie index files (genome)..
[2018-10-13 17:26:11] Checking for reference FASTA file
[2018-10-13 17:26:11] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:26:15] Reading known junctions from GTF file
[2018-10-13 17:26:20] Preparing reads
	 left reads: min. length=100, max. length=100, 102487 kept reads (130 discarded)
	right reads: min. length=100, max. length=100, 102365 kept reads (252 discarded)
[2018-10-13 17:26:24] Building transcriptome data files /scratch/8793395.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:26:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:34:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:35:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:35:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:35:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:35:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:35:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:35:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:36:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:36:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:36:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:36:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:36:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:36:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:36:59] Searching for junctions via segment mapping
[2018-10-13 17:39:33] Retrieving sequences for splices
[2018-10-13 17:41:52] Indexing splices
[2018-10-13 17:42:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:42:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:42:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:42:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:42:27] Joining segment hits
[2018-10-13 17:44:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:44:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:44:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:45:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:45:06] Joining segment hits
[2018-10-13 17:47:29] Reporting output tracks
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[2018-10-13 17:50:01] A summary of the alignment counts can be found in /scratch/8793395.1.linga/tophat2/align_summary.txt
[2018-10-13 17:50:01] Run complete: 00:23:49 elapsed