[2018-10-13 06:27:45] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:27:45] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:27:45] Checking for Bowtie index files (genome)..
[2018-10-13 06:27:45] Checking for reference FASTA file
[2018-10-13 06:27:45] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:27:49] Reading known junctions from GTF file
[2018-10-13 06:27:55] Preparing reads
	 left reads: min. length=100, max. length=100, 486450 kept reads (350 discarded)
	right reads: min. length=100, max. length=100, 486302 kept reads (498 discarded)
[2018-10-13 06:28:18] Building transcriptome data files /scratch/8793055.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:28:38] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:37:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:38:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:38:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:38:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:39:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:39:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:39:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:39:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:39:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:40:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:40:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:40:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:40:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:41:09] Searching for junctions via segment mapping
[2018-10-13 06:45:47] Retrieving sequences for splices
[2018-10-13 06:47:55] Indexing splices
[2018-10-13 06:48:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:48:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:48:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:48:34] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:48:40] Joining segment hits
[2018-10-13 06:51:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:51:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:51:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:51:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:51:23] Joining segment hits
[2018-10-13 06:53:51] Reporting output tracks
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[2018-10-13 07:00:34] A summary of the alignment counts can be found in /scratch/8793055.1.linga/tophat2/align_summary.txt
[2018-10-13 07:00:34] Run complete: 00:32:49 elapsed