[2018-10-12 21:30:59] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:30:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:30:59] Checking for Bowtie index files (genome)..
[2018-10-12 21:30:59] Checking for reference FASTA file
[2018-10-12 21:30:59] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:31:04] Reading known junctions from GTF file
[2018-10-12 21:31:09] Preparing reads
	 left reads: min. length=100, max. length=100, 311851 kept reads (264 discarded)
	right reads: min. length=100, max. length=100, 311859 kept reads (256 discarded)
[2018-10-12 21:31:24] Building transcriptome data files /scratch/8792759.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:31:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:40:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:41:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:41:57] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:41:58] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:42:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:42:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:42:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:43:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:43:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:43:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:44:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:44:16] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:44:27] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:44:38] Searching for junctions via segment mapping
[2018-10-12 21:47:21] Retrieving sequences for splices
[2018-10-12 21:49:32] Indexing splices
[2018-10-12 21:49:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:49:59] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:50:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:50:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:50:14] Joining segment hits
[2018-10-12 21:52:44] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:52:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:52:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:52:58] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:53:03] Joining segment hits
[2018-10-12 21:55:48] Reporting output tracks
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[2018-10-12 21:59:12] A summary of the alignment counts can be found in /scratch/8792759.1.linga/tophat2/align_summary.txt
[2018-10-12 21:59:12] Run complete: 00:28:13 elapsed