[2018-10-13 17:36:02] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:36:02] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:36:02] Checking for Bowtie index files (genome)..
[2018-10-13 17:36:02] Checking for reference FASTA file
[2018-10-13 17:36:02] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:36:07] Reading known junctions from GTF file
[2018-10-13 17:36:11] Preparing reads
	 left reads: min. length=100, max. length=100, 340246 kept reads (284 discarded)
	right reads: min. length=100, max. length=100, 339961 kept reads (569 discarded)
[2018-10-13 17:36:26] Building transcriptome data files /scratch/8793406.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:36:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:44:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:45:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:46:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:46:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:46:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:47:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:47:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:47:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:47:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:48:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:48:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:48:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:49:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:49:12] Searching for junctions via segment mapping
[2018-10-13 17:52:04] Retrieving sequences for splices
[2018-10-13 17:54:17] Indexing splices
[2018-10-13 17:54:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:54:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:54:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:54:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:54:55] Joining segment hits
[2018-10-13 17:57:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:57:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:57:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:57:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:57:30] Joining segment hits
[2018-10-13 17:59:58] Reporting output tracks
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[2018-10-13 18:03:10] A summary of the alignment counts can be found in /scratch/8793406.1.linga/tophat2/align_summary.txt
[2018-10-13 18:03:10] Run complete: 00:27:07 elapsed