[2018-10-13 08:05:05] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:05:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:05:05] Checking for Bowtie index files (genome)..
[2018-10-13 08:05:05] Checking for reference FASTA file
[2018-10-13 08:05:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:05:09] Reading known junctions from GTF file
[2018-10-13 08:05:13] Preparing reads
	 left reads: min. length=100, max. length=100, 761200 kept reads (246 discarded)
	right reads: min. length=100, max. length=100, 761031 kept reads (415 discarded)
[2018-10-13 08:05:44] Building transcriptome data files /scratch/8793105.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:06:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:15:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:16:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:18:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:18:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:19:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:19:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:19:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:19:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:20:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:20:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:20:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:21:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:21:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:21:38] Searching for junctions via segment mapping
[2018-10-13 08:28:27] Retrieving sequences for splices
[2018-10-13 08:30:37] Indexing splices
[2018-10-13 08:31:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:31:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:31:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:31:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:31:40] Joining segment hits
[2018-10-13 08:34:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:34:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:34:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:34:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:34:57] Joining segment hits
[2018-10-13 08:37:34] Reporting output tracks
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[2018-10-13 09:01:02] A summary of the alignment counts can be found in /scratch/8793105.1.linga/tophat2/align_summary.txt
[2018-10-13 09:01:02] Run complete: 00:55:57 elapsed