[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 04:12:20] Preparing reads
	 left reads: min. length=100, max. length=100, 467458 kept reads (267 discarded)
	right reads: min. length=100, max. length=100, 467365 kept reads (360 discarded)
[2018-10-13 04:12:38] Building transcriptome data files /scratch/8792985.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:12:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:21:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:22:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:24:12] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:24:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:24:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:24:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:25:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:25:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:25:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:25:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:26:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:26:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:26:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:26:47] Searching for junctions via segment mapping
[2018-10-13 04:32:40] Retrieving sequences for splices
[2018-10-13 04:34:51] Indexing splices
[2018-10-13 04:35:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:35:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:35:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:35:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:35:46] Joining segment hits
[2018-10-13 04:38:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:38:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:38:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:38:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:38:46] Joining segment hits
[2018-10-13 04:41:21] Reporting output tracks
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[2018-10-13 05:01:07] A summary of the alignment counts can be found in /scratch/8792985.1.linga/tophat2/align_summary.txt
[2018-10-13 05:01:07] Run complete: 00:48:55 elapsed