[2018-10-13 11:03:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:03:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:03:34] Checking for Bowtie index files (genome)..
[2018-10-13 11:03:34] Checking for reference FASTA file
[2018-10-13 11:03:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:03:36] Reading known junctions from GTF file
[2018-10-13 11:03:38] Preparing reads
	 left reads: min. length=100, max. length=100, 666544 kept reads (92 discarded)
	right reads: min. length=100, max. length=100, 666242 kept reads (394 discarded)
[2018-10-13 11:03:57] Building transcriptome data files /scratch/8793192.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:04:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:09:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:10:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:10:30] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:10:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:10:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:10:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:10:59] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:11:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:11:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:11:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:11:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:11:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:11:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:11:48] Searching for junctions via segment mapping
[2018-10-13 11:13:35] Retrieving sequences for splices
[2018-10-13 11:14:47] Indexing splices
[2018-10-13 11:14:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:15:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:15:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:15:07] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:15:09] Joining segment hits
[2018-10-13 11:16:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:16:32] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:16:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:16:38] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:16:40] Joining segment hits
[2018-10-13 11:18:01] Reporting output tracks
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[2018-10-13 11:20:39] A summary of the alignment counts can be found in /scratch/8793192.1.c/tophat2/align_summary.txt
[2018-10-13 11:20:39] Run complete: 00:17:04 elapsed