[2018-10-12 22:29:53] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:29:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:29:53] Checking for Bowtie index files (genome)..
[2018-10-12 22:29:53] Checking for reference FASTA file
[2018-10-12 22:29:53] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:29:57] Reading known junctions from GTF file
[2018-10-12 22:30:01] Preparing reads
	 left reads: min. length=100, max. length=100, 340458 kept reads (225 discarded)
	right reads: min. length=100, max. length=100, 340186 kept reads (497 discarded)
[2018-10-12 22:30:16] Building transcriptome data files /scratch/8792794.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:30:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:38:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:38:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:39:24] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:39:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:39:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:40:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:40:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:40:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:40:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:41:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:41:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:41:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:41:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:41:48] Searching for junctions via segment mapping
[2018-10-12 22:44:24] Retrieving sequences for splices
[2018-10-12 22:46:42] Indexing splices
[2018-10-12 22:47:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:47:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:47:10] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:47:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:47:19] Joining segment hits
[2018-10-12 22:49:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:49:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:49:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:49:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:49:52] Joining segment hits
[2018-10-12 22:52:10] Reporting output tracks
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[2018-10-12 22:55:28] A summary of the alignment counts can be found in /scratch/8792794.1.linga/tophat2/align_summary.txt
[2018-10-12 22:55:28] Run complete: 00:25:34 elapsed