[2018-10-12 21:59:47] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:59:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:59:47] Checking for Bowtie index files (genome)..
[2018-10-12 21:59:47] Checking for reference FASTA file
[2018-10-12 21:59:47] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:59:51] Reading known junctions from GTF file
[2018-10-12 21:59:55] Preparing reads
	 left reads: min. length=100, max. length=100, 444092 kept reads (307 discarded)
	right reads: min. length=100, max. length=100, 443663 kept reads (736 discarded)
[2018-10-12 22:00:13] Building transcriptome data files /scratch/8792775.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:00:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:08:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:09:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:10:20] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:10:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:11:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:11:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:11:24] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:11:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:11:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:12:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:12:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:12:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:13:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:13:11] Searching for junctions via segment mapping
[2018-10-12 22:15:55] Retrieving sequences for splices
[2018-10-12 22:17:56] Indexing splices
[2018-10-12 22:18:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:18:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:18:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:18:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:18:34] Joining segment hits
[2018-10-12 22:20:52] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:20:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:21:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:21:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:21:11] Joining segment hits
[2018-10-12 22:23:28] Reporting output tracks
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[2018-10-12 22:27:02] A summary of the alignment counts can be found in /scratch/8792775.1.linga/tophat2/align_summary.txt
[2018-10-12 22:27:02] Run complete: 00:27:15 elapsed