[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 22:32:45] Reading known junctions from GTF file
[2018-10-12 22:32:49] Preparing reads
	 left reads: min. length=100, max. length=100, 429884 kept reads (330 discarded)
	right reads: min. length=100, max. length=100, 429479 kept reads (735 discarded)
[2018-10-12 22:33:08] Building transcriptome data files /scratch/8792800.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:33:28] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:41:29] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:42:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:42:57] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:42:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:43:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:43:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:44:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:44:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:44:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:45:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:45:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:45:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:45:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:46:04] Searching for junctions via segment mapping
[2018-10-12 22:48:50] Retrieving sequences for splices
[2018-10-12 22:50:59] Indexing splices
[2018-10-12 22:51:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:51:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:51:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:51:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:51:37] Joining segment hits
[2018-10-12 22:54:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:54:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:54:17] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:54:21] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:54:25] Joining segment hits
[2018-10-12 22:56:56] Reporting output tracks
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[2018-10-12 23:00:27] A summary of the alignment counts can be found in /scratch/8792800.1.linga/tophat2/align_summary.txt
[2018-10-12 23:00:27] Run complete: 00:27:46 elapsed