[2018-10-12 21:30:57] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:30:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:30:57] Checking for Bowtie index files (genome)..
[2018-10-12 21:30:57] Checking for reference FASTA file
[2018-10-12 21:30:57] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:31:01] Reading known junctions from GTF file
[2018-10-12 21:31:06] Preparing reads
	 left reads: min. length=100, max. length=100, 441640 kept reads (296 discarded)
	right reads: min. length=100, max. length=100, 441185 kept reads (751 discarded)
[2018-10-12 21:31:25] Building transcriptome data files /scratch/8792755.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:31:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:39:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:40:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:41:08] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:41:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:41:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:41:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:42:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:42:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:42:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:43:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:43:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:43:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:43:50] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:44:01] Searching for junctions via segment mapping
[2018-10-12 21:46:54] Retrieving sequences for splices
[2018-10-12 21:49:04] Indexing splices
[2018-10-12 21:49:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:49:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:49:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:49:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:49:44] Joining segment hits
[2018-10-12 21:52:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:52:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:52:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:52:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:52:38] Joining segment hits
[2018-10-12 21:55:10] Reporting output tracks
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[2018-10-12 21:58:43] A summary of the alignment counts can be found in /scratch/8792755.1.linga/tophat2/align_summary.txt
[2018-10-12 21:58:43] Run complete: 00:27:46 elapsed