[2018-10-13 16:28:38] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:28:38] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:28:38] Checking for Bowtie index files (genome)..
[2018-10-13 16:28:38] Checking for reference FASTA file
[2018-10-13 16:28:38] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:28:44] Reading known junctions from GTF file
[2018-10-13 16:28:49] Preparing reads
	 left reads: min. length=100, max. length=100, 253207 kept reads (228 discarded)
	right reads: min. length=100, max. length=100, 252998 kept reads (437 discarded)
[2018-10-13 16:29:00] Building transcriptome data files /scratch/8793356.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:29:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:37:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:38:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:38:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:38:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:39:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:39:29] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:39:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:39:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:39:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:40:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:40:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:40:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:40:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:41:00] Searching for junctions via segment mapping
[2018-10-13 16:44:11] Retrieving sequences for splices
[2018-10-13 16:46:26] Indexing splices
[2018-10-13 16:46:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:46:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:46:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:47:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:47:06] Joining segment hits
[2018-10-13 16:49:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:49:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:49:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:49:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:49:51] Joining segment hits
[2018-10-13 16:52:19] Reporting output tracks
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[2018-10-13 16:56:48] A summary of the alignment counts can be found in /scratch/8793356.1.linga/tophat2/align_summary.txt
[2018-10-13 16:56:48] Run complete: 00:28:10 elapsed