[2018-10-12 21:33:29] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:33:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:33:29] Checking for Bowtie index files (genome)..
[2018-10-12 21:33:29] Checking for reference FASTA file
[2018-10-12 21:33:29] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:33:33] Reading known junctions from GTF file
[2018-10-12 21:33:38] Preparing reads
	 left reads: min. length=100, max. length=100, 249211 kept reads (227 discarded)
	right reads: min. length=100, max. length=100, 248910 kept reads (528 discarded)
[2018-10-12 21:33:49] Building transcriptome data files /scratch/8792760.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:34:10] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:42:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:43:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:43:46] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:43:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:44:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:44:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:44:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:44:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:44:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:45:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:45:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:45:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:45:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:46:07] Searching for junctions via segment mapping
[2018-10-12 21:48:49] Retrieving sequences for splices
[2018-10-12 21:51:00] Indexing splices
[2018-10-12 21:51:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:51:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:51:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:51:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:51:37] Joining segment hits
[2018-10-12 21:54:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:54:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:54:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:54:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:54:23] Joining segment hits
[2018-10-12 21:56:50] Reporting output tracks
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[2018-10-12 21:59:46] A summary of the alignment counts can be found in /scratch/8792760.1.linga/tophat2/align_summary.txt
[2018-10-12 21:59:46] Run complete: 00:26:16 elapsed