[2018-10-13 06:10:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:10:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:10:40] Checking for Bowtie index files (genome)..
[2018-10-13 06:10:40] Checking for reference FASTA file
[2018-10-13 06:10:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:10:44] Reading known junctions from GTF file
[2018-10-13 06:10:48] Preparing reads
	 left reads: min. length=100, max. length=100, 821987 kept reads (95 discarded)
	right reads: min. length=100, max. length=100, 821717 kept reads (365 discarded)
[2018-10-13 06:11:21] Building transcriptome data files /scratch/8793047.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:11:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:19:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:20:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:21:27] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:21:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:21:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:22:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:22:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:22:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:22:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:23:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:23:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:23:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:23:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:23:44] Searching for junctions via segment mapping
[2018-10-13 06:28:23] Retrieving sequences for splices
[2018-10-13 06:30:24] Indexing splices
[2018-10-13 06:30:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:30:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:30:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:31:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:31:12] Joining segment hits
[2018-10-13 06:33:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:33:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:33:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:33:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:33:57] Joining segment hits
[2018-10-13 06:36:15] Reporting output tracks
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[2018-10-13 06:49:42] A summary of the alignment counts can be found in /scratch/8793047.1.linga/tophat2/align_summary.txt
[2018-10-13 06:49:42] Run complete: 00:39:02 elapsed