[2018-10-12 21:01:13] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:01:13] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:01:14] Checking for Bowtie index files (genome)..
[2018-10-12 21:01:14] Checking for reference FASTA file
[2018-10-12 21:01:14] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:01:19] Reading known junctions from GTF file
[2018-10-12 21:01:24] Preparing reads
	 left reads: min. length=100, max. length=100, 209605 kept reads (118 discarded)
	right reads: min. length=100, max. length=100, 209369 kept reads (354 discarded)
[2018-10-12 21:01:35] Building transcriptome data files /scratch/8792742.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:01:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:10:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:11:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:11:49] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:11:49] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:12:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:12:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:12:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:12:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:12:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:13:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:13:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:13:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:13:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:14:07] Searching for junctions via segment mapping
[2018-10-12 21:16:48] Retrieving sequences for splices
[2018-10-12 21:19:06] Indexing splices
[2018-10-12 21:19:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:19:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:19:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:19:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:19:42] Joining segment hits
[2018-10-12 21:22:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:22:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:22:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:22:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:22:33] Joining segment hits
[2018-10-12 21:24:56] Reporting output tracks
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[2018-10-12 21:27:58] A summary of the alignment counts can be found in /scratch/8792742.1.linga/tophat2/align_summary.txt
[2018-10-12 21:27:58] Run complete: 00:26:44 elapsed