[2018-10-13 11:11:47] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:11:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:11:47] Checking for Bowtie index files (genome)..
[2018-10-13 11:11:47] Checking for reference FASTA file
[2018-10-13 11:11:47] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:11:51] Reading known junctions from GTF file
[2018-10-13 11:11:56] Preparing reads
	 left reads: min. length=100, max. length=100, 820691 kept reads (66 discarded)
	right reads: min. length=100, max. length=100, 820445 kept reads (312 discarded)
[2018-10-13 11:12:28] Building transcriptome data files /scratch/8793196.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:12:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:20:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:21:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:21:40] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:21:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:22:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:22:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:22:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:22:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:22:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:23:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:23:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:23:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:23:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:24:04] Searching for junctions via segment mapping
[2018-10-13 11:27:26] Retrieving sequences for splices
[2018-10-13 11:29:26] Indexing splices
[2018-10-13 11:29:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:29:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:29:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:30:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:30:04] Joining segment hits
[2018-10-13 11:32:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:32:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:32:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:32:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:32:41] Joining segment hits
[2018-10-13 11:34:57] Reporting output tracks
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[2018-10-13 11:40:38] A summary of the alignment counts can be found in /scratch/8793196.1.linga/tophat2/align_summary.txt
[2018-10-13 11:40:38] Run complete: 00:28:51 elapsed