[2018-10-13 16:04:42] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:04:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:04:42] Checking for Bowtie index files (genome)..
[2018-10-13 16:04:42] Checking for reference FASTA file
[2018-10-13 16:04:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:04:47] Reading known junctions from GTF file
[2018-10-13 16:04:52] Preparing reads
	 left reads: min. length=100, max. length=100, 345878 kept reads (322 discarded)
	right reads: min. length=100, max. length=100, 345831 kept reads (369 discarded)
[2018-10-13 16:05:08] Building transcriptome data files /scratch/8793343.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:05:28] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:13:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:14:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:14:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:14:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:15:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:15:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:15:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:15:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:15:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:16:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:16:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:16:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:16:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:16:39] Searching for junctions via segment mapping
[2018-10-13 16:19:36] Retrieving sequences for splices
[2018-10-13 16:21:51] Indexing splices
[2018-10-13 16:22:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:22:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:22:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:22:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:22:30] Joining segment hits
[2018-10-13 16:24:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:24:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:24:55] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:25:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:25:04] Joining segment hits
[2018-10-13 16:27:32] Reporting output tracks
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[2018-10-13 16:31:20] A summary of the alignment counts can be found in /scratch/8793343.1.linga/tophat2/align_summary.txt
[2018-10-13 16:31:20] Run complete: 00:26:38 elapsed