[2018-10-13 17:29:42] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:29:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:29:42] Checking for Bowtie index files (genome)..
[2018-10-13 17:29:42] Checking for reference FASTA file
[2018-10-13 17:29:42] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:29:46] Reading known junctions from GTF file
[2018-10-13 17:29:51] Preparing reads
	 left reads: min. length=100, max. length=100, 184255 kept reads (204 discarded)
	right reads: min. length=100, max. length=100, 184044 kept reads (415 discarded)
[2018-10-13 17:29:59] Building transcriptome data files /scratch/8793399.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:30:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:38:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:38:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:38:55] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:38:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:39:14] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:39:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:39:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:39:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:39:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:40:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:40:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:40:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:40:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:40:43] Searching for junctions via segment mapping
[2018-10-13 17:43:11] Retrieving sequences for splices
[2018-10-13 17:45:21] Indexing splices
[2018-10-13 17:45:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:45:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:45:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:45:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:45:58] Joining segment hits
[2018-10-13 17:48:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:48:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:48:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:48:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:48:30] Joining segment hits
[2018-10-13 17:50:50] Reporting output tracks
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[2018-10-13 17:53:41] A summary of the alignment counts can be found in /scratch/8793399.1.linga/tophat2/align_summary.txt
[2018-10-13 17:53:41] Run complete: 00:23:58 elapsed