[2018-10-13 17:13:18] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:13:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:13:18] Checking for Bowtie index files (genome)..
[2018-10-13 17:13:18] Checking for reference FASTA file
[2018-10-13 17:13:18] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:13:21] Reading known junctions from GTF file
[2018-10-13 17:13:25] Preparing reads
	 left reads: min. length=100, max. length=100, 344804 kept reads (302 discarded)
	right reads: min. length=100, max. length=100, 344535 kept reads (571 discarded)
[2018-10-13 17:13:39] Building transcriptome data files /scratch/8793389.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:13:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:21:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:22:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:22:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:22:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:23:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:23:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:23:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:23:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:23:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:24:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:24:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:24:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:24:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:24:41] Searching for junctions via segment mapping
[2018-10-13 17:27:28] Retrieving sequences for splices
[2018-10-13 17:29:37] Indexing splices
[2018-10-13 17:29:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:30:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:30:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:30:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:30:13] Joining segment hits
[2018-10-13 17:32:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:32:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:32:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:32:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:32:46] Joining segment hits
[2018-10-13 17:34:50] Reporting output tracks
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[2018-10-13 17:38:12] A summary of the alignment counts can be found in /scratch/8793389.1.linga/tophat2/align_summary.txt
[2018-10-13 17:38:12] Run complete: 00:24:53 elapsed