[2018-10-13 17:19:19] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:19:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:19:19] Checking for Bowtie index files (genome)..
[2018-10-13 17:19:19] Checking for reference FASTA file
[2018-10-13 17:19:19] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:19:23] Reading known junctions from GTF file
[2018-10-13 17:19:27] Preparing reads
	 left reads: min. length=100, max. length=100, 385223 kept reads (194 discarded)
	right reads: min. length=100, max. length=100, 384904 kept reads (513 discarded)
[2018-10-13 17:19:42] Building transcriptome data files /scratch/8793391.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:20:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:27:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:28:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:28:46] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:28:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:29:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:29:26] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:29:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:29:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:29:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:30:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:30:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:30:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:31:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:31:10] Searching for junctions via segment mapping
[2018-10-13 17:33:59] Retrieving sequences for splices
[2018-10-13 17:36:04] Indexing splices
[2018-10-13 17:36:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:36:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:36:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:36:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:36:42] Joining segment hits
[2018-10-13 17:39:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:39:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:39:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:39:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:39:20] Joining segment hits
[2018-10-13 17:41:39] Reporting output tracks
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[2018-10-13 17:45:13] A summary of the alignment counts can be found in /scratch/8793391.1.linga/tophat2/align_summary.txt
[2018-10-13 17:45:13] Run complete: 00:25:54 elapsed