[2018-10-13 04:01:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:01:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:01:29] Checking for Bowtie index files (genome)..
[2018-10-13 04:01:29] Checking for reference FASTA file
[2018-10-13 04:01:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:01:34] Reading known junctions from GTF file
[2018-10-13 04:01:39] Preparing reads
	 left reads: min. length=100, max. length=100, 1516336 kept reads (102 discarded)
	right reads: min. length=100, max. length=100, 1516035 kept reads (403 discarded)
[2018-10-13 04:02:42] Building transcriptome data files /scratch/8792980.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:03:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:10:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:12:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:13:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:13:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:14:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:14:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:14:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:14:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:15:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:16:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:16:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:16:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:16:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:17:06] Searching for junctions via segment mapping
[2018-10-13 04:22:43] Retrieving sequences for splices
[2018-10-13 04:24:54] Indexing splices
[2018-10-13 04:25:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:25:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:25:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:25:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:25:47] Joining segment hits
[2018-10-13 04:28:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:28:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:28:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:28:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:28:54] Joining segment hits
[2018-10-13 04:31:35] Reporting output tracks
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[2018-10-13 04:44:39] A summary of the alignment counts can be found in /scratch/8792980.1.linga/tophat2/align_summary.txt
[2018-10-13 04:44:39] Run complete: 00:43:10 elapsed