[2018-10-13 06:51:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:51:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:51:08] Checking for Bowtie index files (genome)..
[2018-10-13 06:51:08] Checking for reference FASTA file
[2018-10-13 06:51:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:51:12] Reading known junctions from GTF file
[2018-10-13 06:51:17] Preparing reads
	 left reads: min. length=100, max. length=100, 293349 kept reads (177 discarded)
	right reads: min. length=100, max. length=100, 293115 kept reads (411 discarded)
[2018-10-13 06:51:29] Building transcriptome data files /scratch/8793068.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:51:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:59:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:00:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:00:40] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:00:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:01:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:01:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:01:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:01:30] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:01:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:02:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:02:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:02:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:02:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:02:37] Searching for junctions via segment mapping
[2018-10-13 07:05:46] Retrieving sequences for splices
[2018-10-13 07:07:57] Indexing splices
[2018-10-13 07:08:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:08:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:08:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:08:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:08:36] Joining segment hits
[2018-10-13 07:10:55] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:11:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:11:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:11:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:11:14] Joining segment hits
[2018-10-13 07:13:29] Reporting output tracks
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[2018-10-13 07:17:50] A summary of the alignment counts can be found in /scratch/8793068.1.linga/tophat2/align_summary.txt
[2018-10-13 07:17:50] Run complete: 00:26:41 elapsed