[2018-10-12 21:33:34] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:33:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:33:34] Checking for Bowtie index files (genome)..
[2018-10-12 21:33:34] Checking for reference FASTA file
[2018-10-12 21:33:34] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:33:38] Reading known junctions from GTF file
[2018-10-12 21:33:43] Preparing reads
	 left reads: min. length=100, max. length=100, 451429 kept reads (385 discarded)
	right reads: min. length=100, max. length=100, 451471 kept reads (343 discarded)
[2018-10-12 21:34:02] Building transcriptome data files /scratch/8792762.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:34:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:42:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:42:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:43:38] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:43:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:44:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:44:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:44:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:44:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:45:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:45:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:45:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:46:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:46:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:46:31] Searching for junctions via segment mapping
[2018-10-12 21:49:22] Retrieving sequences for splices
[2018-10-12 21:51:23] Indexing splices
[2018-10-12 21:51:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:51:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:51:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:51:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:52:00] Joining segment hits
[2018-10-12 21:54:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:54:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:54:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:54:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:54:38] Joining segment hits
[2018-10-12 21:56:59] Reporting output tracks
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[2018-10-12 22:00:30] A summary of the alignment counts can be found in /scratch/8792762.1.linga/tophat2/align_summary.txt
[2018-10-12 22:00:30] Run complete: 00:26:56 elapsed