[2018-10-12 22:10:48] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:10:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:10:48] Checking for Bowtie index files (genome)..
[2018-10-12 22:10:48] Checking for reference FASTA file
[2018-10-12 22:10:48] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:10:52] Reading known junctions from GTF file
[2018-10-12 22:10:57] Preparing reads
	 left reads: min. length=100, max. length=100, 271458 kept reads (175 discarded)
	right reads: min. length=100, max. length=100, 271186 kept reads (447 discarded)
[2018-10-12 22:11:10] Building transcriptome data files /scratch/8792785.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:11:38] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:25:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:25:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:26:32] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:26:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:27:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:27:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:27:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:27:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:27:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:28:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:28:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:28:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:29:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:29:18] Searching for junctions via segment mapping
[2018-10-12 22:32:05] Retrieving sequences for splices
[2018-10-12 22:34:25] Indexing splices
[2018-10-12 22:34:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:34:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:34:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:35:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:35:06] Joining segment hits
[2018-10-12 22:38:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:38:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:38:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:38:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:38:36] Joining segment hits
[2018-10-12 22:41:34] Reporting output tracks
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[2018-10-12 22:45:22] A summary of the alignment counts can be found in /scratch/8792785.1.linga/tophat2/align_summary.txt
[2018-10-12 22:45:22] Run complete: 00:34:34 elapsed