[2018-10-13 17:04:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:04:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:04:56] Checking for Bowtie index files (genome)..
[2018-10-13 17:04:56] Checking for reference FASTA file
[2018-10-13 17:04:56] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:05:00] Reading known junctions from GTF file
[2018-10-13 17:05:04] Preparing reads
	 left reads: min. length=100, max. length=100, 508147 kept reads (370 discarded)
	right reads: min. length=100, max. length=100, 507770 kept reads (747 discarded)
[2018-10-13 17:05:25] Building transcriptome data files /scratch/8793385.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:05:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:13:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:14:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:15:12] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:15:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:16:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:16:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:16:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:16:38] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:16:49] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:17:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:17:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:18:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:18:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:18:30] Searching for junctions via segment mapping
[2018-10-13 17:21:15] Retrieving sequences for splices
[2018-10-13 17:23:14] Indexing splices
[2018-10-13 17:23:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:23:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:23:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:23:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:23:54] Joining segment hits
[2018-10-13 17:26:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:26:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:26:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:26:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:26:35] Joining segment hits
[2018-10-13 17:29:00] Reporting output tracks
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[2018-10-13 17:32:42] A summary of the alignment counts can be found in /scratch/8793385.1.linga/tophat2/align_summary.txt
[2018-10-13 17:32:42] Run complete: 00:27:45 elapsed