[2018-10-12 23:15:15] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:15:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:15:15] Checking for Bowtie index files (genome)..
[2018-10-12 23:15:15] Checking for reference FASTA file
[2018-10-12 23:15:15] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:15:20] Reading known junctions from GTF file
[2018-10-12 23:15:24] Preparing reads
	 left reads: min. length=100, max. length=100, 309250 kept reads (198 discarded)
	right reads: min. length=100, max. length=100, 308923 kept reads (525 discarded)
[2018-10-12 23:15:38] Building transcriptome data files /scratch/8792830.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:15:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:24:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:25:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:25:45] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:25:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:26:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:26:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:26:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:26:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:27:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:27:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:27:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:28:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:28:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:28:29] Searching for junctions via segment mapping
[2018-10-12 23:31:08] Retrieving sequences for splices
[2018-10-12 23:33:21] Indexing splices
[2018-10-12 23:33:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:33:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:33:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:33:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:33:59] Joining segment hits
[2018-10-12 23:36:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:36:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:36:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:36:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:36:39] Joining segment hits
[2018-10-12 23:39:02] Reporting output tracks
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[2018-10-12 23:42:53] A summary of the alignment counts can be found in /scratch/8792830.1.linga/tophat2/align_summary.txt
[2018-10-12 23:42:53] Run complete: 00:27:36 elapsed