[2018-10-13 11:03:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:03:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:03:41] Checking for Bowtie index files (genome)..
[2018-10-13 11:03:41] Checking for reference FASTA file
[2018-10-13 11:03:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:03:46] Reading known junctions from GTF file
[2018-10-13 11:03:50] Preparing reads
	 left reads: min. length=100, max. length=100, 901061 kept reads (76 discarded)
	right reads: min. length=100, max. length=100, 900930 kept reads (207 discarded)
[2018-10-13 11:04:29] Building transcriptome data files /scratch/8793190.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:04:49] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:13:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:13:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:14:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:14:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:15:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:15:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:15:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:15:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:15:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:16:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:16:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:16:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:17:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:17:12] Searching for junctions via segment mapping
[2018-10-13 11:20:16] Retrieving sequences for splices
[2018-10-13 11:23:13] Indexing splices
[2018-10-13 11:23:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:23:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:23:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:23:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:23:55] Joining segment hits
[2018-10-13 11:26:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:26:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:26:35] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:26:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:26:44] Joining segment hits
[2018-10-13 11:29:13] Reporting output tracks
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[2018-10-13 11:34:58] A summary of the alignment counts can be found in /scratch/8793190.1.linga/tophat2/align_summary.txt
[2018-10-13 11:34:58] Run complete: 00:31:16 elapsed