[2018-10-12 22:46:49] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:46:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:46:49] Checking for Bowtie index files (genome)..
[2018-10-12 22:46:49] Checking for reference FASTA file
[2018-10-12 22:46:49] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:46:52] Reading known junctions from GTF file
[2018-10-12 22:46:57] Preparing reads
	 left reads: min. length=100, max. length=100, 355684 kept reads (231 discarded)
	right reads: min. length=100, max. length=100, 355241 kept reads (674 discarded)
[2018-10-12 22:47:12] Building transcriptome data files /scratch/8792808.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:47:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:55:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:56:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:56:46] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:56:46] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:57:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:57:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:57:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:57:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:58:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:58:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:58:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:59:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:59:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:59:34] Searching for junctions via segment mapping
[2018-10-12 23:02:18] Retrieving sequences for splices
[2018-10-12 23:04:27] Indexing splices
[2018-10-12 23:04:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:04:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:04:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:04:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:05:03] Joining segment hits
[2018-10-12 23:07:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:07:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:07:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:07:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:07:39] Joining segment hits
[2018-10-12 23:09:57] Reporting output tracks
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[2018-10-12 23:13:20] A summary of the alignment counts can be found in /scratch/8792808.1.linga/tophat2/align_summary.txt
[2018-10-12 23:13:20] Run complete: 00:26:31 elapsed