[2018-10-13 07:14:55] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:14:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:14:55] Checking for Bowtie index files (genome)..
[2018-10-13 07:14:55] Checking for reference FASTA file
[2018-10-13 07:14:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:14:57] Reading known junctions from GTF file
[2018-10-13 07:14:59] Preparing reads
	 left reads: min. length=100, max. length=100, 609197 kept reads (2484 discarded)
	right reads: min. length=100, max. length=100, 609025 kept reads (2656 discarded)
[2018-10-13 07:15:16] Building transcriptome data files /scratch/8793080.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:15:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:20:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:22:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:23:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:23:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:24:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:24:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:24:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:24:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:24:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:25:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:25:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:25:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:26:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:26:20] Searching for junctions via segment mapping
[2018-10-13 07:28:45] Retrieving sequences for splices
[2018-10-13 07:29:57] Indexing splices
Building a SMALL index
[2018-10-13 07:30:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:30:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:30:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:30:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:30:23] Joining segment hits
[2018-10-13 07:31:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:31:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:31:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:31:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:32:01] Joining segment hits
[2018-10-13 07:33:24] Reporting output tracks
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[2018-10-13 07:36:09] A summary of the alignment counts can be found in /scratch/8793080.1.c/tophat2/align_summary.txt
[2018-10-13 07:36:09] Run complete: 00:21:14 elapsed
[samopen] SAM header is present: 114 sequences.