[2018-10-13 13:48:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:48:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:48:42] Checking for Bowtie index files (genome)..
[2018-10-13 13:48:42] Checking for reference FASTA file
[2018-10-13 13:48:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:48:45] Reading known junctions from GTF file
[2018-10-13 13:48:49] Preparing reads
	 left reads: min. length=100, max. length=100, 1059559 kept reads (83 discarded)
	right reads: min. length=100, max. length=100, 1059243 kept reads (399 discarded)
[2018-10-13 13:49:32] Building transcriptome data files /scratch/8793272.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:49:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:57:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:58:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:59:38] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:59:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:00:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:00:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:00:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:00:39] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:00:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:01:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:01:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:01:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:01:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:02:08] Searching for junctions via segment mapping
[2018-10-13 14:06:52] Retrieving sequences for splices
[2018-10-13 14:08:51] Indexing splices
[2018-10-13 14:09:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:09:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:09:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:09:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:09:38] Joining segment hits
[2018-10-13 14:12:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:12:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:12:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:12:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:12:32] Joining segment hits
[2018-10-13 14:14:56] Reporting output tracks
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[2018-10-13 14:27:26] A summary of the alignment counts can be found in /scratch/8793272.1.linga/tophat2/align_summary.txt
[2018-10-13 14:27:26] Run complete: 00:38:44 elapsed