[2018-10-12 22:43:53] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:43:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:43:53] Checking for Bowtie index files (genome)..
[2018-10-12 22:43:53] Checking for reference FASTA file
[2018-10-12 22:43:53] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:43:57] Reading known junctions from GTF file
[2018-10-12 22:44:02] Preparing reads
	 left reads: min. length=100, max. length=100, 329647 kept reads (199 discarded)
	right reads: min. length=100, max. length=100, 329275 kept reads (571 discarded)
[2018-10-12 22:44:17] Building transcriptome data files /scratch/8792807.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:44:38] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:53:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:54:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:55:00] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:55:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:55:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:55:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:55:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:56:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:56:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:56:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:57:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:57:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:57:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:57:41] Searching for junctions via segment mapping
[2018-10-12 23:00:22] Retrieving sequences for splices
[2018-10-12 23:02:36] Indexing splices
[2018-10-12 23:02:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:03:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:03:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:03:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:03:14] Joining segment hits
[2018-10-12 23:05:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:05:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:05:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:05:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:05:48] Joining segment hits
[2018-10-12 23:08:06] Reporting output tracks
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[2018-10-12 23:11:33] A summary of the alignment counts can be found in /scratch/8792807.1.linga/tophat2/align_summary.txt
[2018-10-12 23:11:33] Run complete: 00:27:40 elapsed