[2018-10-13 18:34:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:34:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:34:32] Checking for Bowtie index files (genome)..
[2018-10-13 18:34:32] Checking for reference FASTA file
[2018-10-13 18:34:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:34:37] Reading known junctions from GTF file
[2018-10-13 18:34:41] Preparing reads
	 left reads: min. length=100, max. length=100, 375322 kept reads (192 discarded)
	right reads: min. length=100, max. length=100, 375009 kept reads (505 discarded)
[2018-10-13 18:34:58] Building transcriptome data files /scratch/8793442.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:35:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:42:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:43:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:43:55] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:43:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:44:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:44:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:44:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:44:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:45:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:45:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:45:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:46:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:46:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:46:25] Searching for junctions via segment mapping
[2018-10-13 18:49:06] Retrieving sequences for splices
[2018-10-13 18:51:12] Indexing splices
[2018-10-13 18:51:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:51:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:51:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:51:46] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:51:50] Joining segment hits
[2018-10-13 18:54:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:54:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:54:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:54:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:54:29] Joining segment hits
[2018-10-13 18:56:46] Reporting output tracks
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[2018-10-13 18:59:51] A summary of the alignment counts can be found in /scratch/8793442.1.linga/tophat2/align_summary.txt
[2018-10-13 18:59:51] Run complete: 00:25:19 elapsed