[2018-10-13 16:24:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:24:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:24:29] Checking for Bowtie index files (genome)..
[2018-10-13 16:24:29] Checking for reference FASTA file
[2018-10-13 16:24:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:24:34] Reading known junctions from GTF file
[2018-10-13 16:24:38] Preparing reads
	 left reads: min. length=100, max. length=100, 48420 kept reads (69 discarded)
	right reads: min. length=100, max. length=100, 48398 kept reads (91 discarded)
[2018-10-13 16:24:40] Building transcriptome data files /scratch/8793351.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:25:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:33:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:34:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:34:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:34:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:34:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:34:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:34:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:34:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:34:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:34:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:35:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:35:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:35:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:35:26] Searching for junctions via segment mapping
[2018-10-13 16:37:41] Retrieving sequences for splices
[2018-10-13 16:39:40] Indexing splices
[2018-10-13 16:39:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:40:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:40:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:40:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:40:15] Joining segment hits
[2018-10-13 16:42:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:42:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:42:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:42:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:42:55] Joining segment hits
[2018-10-13 16:44:57] Reporting output tracks
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[2018-10-13 16:47:16] A summary of the alignment counts can be found in /scratch/8793351.1.linga/tophat2/align_summary.txt
[2018-10-13 16:47:16] Run complete: 00:22:47 elapsed