[2018-10-12 22:01:58] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:01:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:01:58] Checking for Bowtie index files (genome)..
[2018-10-12 22:01:58] Checking for reference FASTA file
[2018-10-12 22:01:58] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:02:02] Reading known junctions from GTF file
[2018-10-12 22:02:07] Preparing reads
	 left reads: min. length=100, max. length=100, 378084 kept reads (260 discarded)
	right reads: min. length=100, max. length=100, 377767 kept reads (577 discarded)
[2018-10-12 22:02:25] Building transcriptome data files /scratch/8792780.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:02:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:10:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:11:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:22] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:12:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:13:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:13:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:13:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:13:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:13:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:14:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:14:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:15:02] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:15:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:15:24] Searching for junctions via segment mapping
[2018-10-12 22:18:17] Retrieving sequences for splices
[2018-10-12 22:20:30] Indexing splices
[2018-10-12 22:20:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:20:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:21:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:21:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:21:09] Joining segment hits
[2018-10-12 22:23:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:23:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:23:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:23:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:23:50] Joining segment hits
[2018-10-12 22:26:13] Reporting output tracks
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[2018-10-12 22:29:58] A summary of the alignment counts can be found in /scratch/8792780.1.linga/tophat2/align_summary.txt
[2018-10-12 22:29:58] Run complete: 00:28:00 elapsed