[2018-10-12 21:30:56] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:30:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:30:56] Checking for Bowtie index files (genome)..
[2018-10-12 21:30:56] Checking for reference FASTA file
[2018-10-12 21:30:56] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:31:00] Reading known junctions from GTF file
[2018-10-12 21:31:04] Preparing reads
	 left reads: min. length=100, max. length=100, 359936 kept reads (175 discarded)
	right reads: min. length=100, max. length=100, 359690 kept reads (421 discarded)
[2018-10-12 21:31:18] Building transcriptome data files /scratch/8792754.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:31:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:40:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:40:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:41:27] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:41:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:42:05] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:42:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:42:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:42:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:42:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:43:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:43:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:43:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:44:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:44:10] Searching for junctions via segment mapping
[2018-10-12 21:47:00] Retrieving sequences for splices
[2018-10-12 21:49:00] Indexing splices
[2018-10-12 21:49:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:49:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:49:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:49:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:49:40] Joining segment hits
[2018-10-12 21:51:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:52:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:52:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:52:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:52:16] Joining segment hits
[2018-10-12 21:54:33] Reporting output tracks
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[2018-10-12 21:57:38] A summary of the alignment counts can be found in /scratch/8792754.1.linga/tophat2/align_summary.txt
[2018-10-12 21:57:38] Run complete: 00:26:41 elapsed