[2018-10-13 04:12:12] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:12:12] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:12:12] Checking for Bowtie index files (genome)..
[2018-10-13 04:12:12] Checking for reference FASTA file
[2018-10-13 04:12:12] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:12:16] Reading known junctions from GTF file
[2018-10-13 04:12:21] Preparing reads
	 left reads: min. length=100, max. length=100, 1128734 kept reads (77 discarded)
	right reads: min. length=100, max. length=100, 1128505 kept reads (306 discarded)
[2018-10-13 04:13:11] Building transcriptome data files /scratch/8792986.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:13:30] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:21:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:22:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:23:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:23:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:24:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:24:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:24:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:24:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:24:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:25:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:25:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:25:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:25:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:26:03] Searching for junctions via segment mapping
[2018-10-13 04:30:24] Retrieving sequences for splices
[2018-10-13 04:32:34] Indexing splices
[2018-10-13 04:32:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:33:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:33:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:33:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:33:17] Joining segment hits
[2018-10-13 04:35:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:35:52] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:35:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:36:04] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:36:09] Joining segment hits
[2018-10-13 04:38:40] Reporting output tracks
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[2018-10-13 04:45:47] A summary of the alignment counts can be found in /scratch/8792986.1.linga/tophat2/align_summary.txt
[2018-10-13 04:45:47] Run complete: 00:33:35 elapsed