[2018-10-12 22:32:41] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:32:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:32:41] Checking for Bowtie index files (genome)..
[2018-10-12 22:32:41] Checking for reference FASTA file
[2018-10-12 22:32:41] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:32:46] Reading known junctions from GTF file
[2018-10-12 22:32:50] Preparing reads
	 left reads: min. length=100, max. length=100, 495383 kept reads (243 discarded)
	right reads: min. length=100, max. length=100, 495023 kept reads (603 discarded)
[2018-10-12 22:33:13] Building transcriptome data files /scratch/8792798.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:33:31] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:41:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:42:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:43:18] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:43:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:44:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:44:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:44:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:44:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:44:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:45:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:45:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:46:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:46:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:46:31] Searching for junctions via segment mapping
[2018-10-12 22:49:20] Retrieving sequences for splices
[2018-10-12 22:51:28] Indexing splices
[2018-10-12 22:51:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:51:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:52:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:52:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:52:11] Joining segment hits
[2018-10-12 22:54:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:54:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:54:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:54:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:55:03] Joining segment hits
[2018-10-12 22:57:34] Reporting output tracks
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[2018-10-12 23:01:45] A summary of the alignment counts can be found in /scratch/8792798.1.linga/tophat2/align_summary.txt
[2018-10-12 23:01:45] Run complete: 00:29:04 elapsed