[2018-10-13 13:53:14] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:53:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:53:14] Checking for Bowtie index files (genome)..
[2018-10-13 13:53:14] Checking for reference FASTA file
[2018-10-13 13:53:14] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:53:16] Reading known junctions from GTF file
[2018-10-13 13:53:18] Preparing reads
	 left reads: min. length=100, max. length=100, 590027 kept reads (194 discarded)
	right reads: min. length=100, max. length=100, 589968 kept reads (253 discarded)
[2018-10-13 13:53:35] Building transcriptome data files /scratch/8793274.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:53:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:59:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:59:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:00:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:00:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:00:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:00:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:00:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:00:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:00:47] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:01:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:01:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:01:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:01:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:01:27] Searching for junctions via segment mapping
[2018-10-13 14:03:58] Retrieving sequences for splices
[2018-10-13 14:05:11] Indexing splices
[2018-10-13 14:05:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:05:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:05:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:05:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:05:36] Joining segment hits
[2018-10-13 14:06:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:07:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:07:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:07:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:07:10] Joining segment hits
[2018-10-13 14:08:31] Reporting output tracks
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[2018-10-13 14:14:11] A summary of the alignment counts can be found in /scratch/8793274.1.c/tophat2/align_summary.txt
[2018-10-13 14:14:11] Run complete: 00:20:57 elapsed