[2018-10-12 22:35:26] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:35:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:35:26] Checking for Bowtie index files (genome)..
[2018-10-12 22:35:26] Checking for reference FASTA file
[2018-10-12 22:35:26] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:35:30] Reading known junctions from GTF file
[2018-10-12 22:35:34] Preparing reads
	 left reads: min. length=100, max. length=100, 407083 kept reads (374 discarded)
	right reads: min. length=100, max. length=100, 406979 kept reads (478 discarded)
[2018-10-12 22:35:51] Building transcriptome data files /scratch/8792803.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:36:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:44:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:44:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:45:32] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:45:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:46:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:46:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:46:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:46:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:46:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:47:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:47:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:48:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:48:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:48:31] Searching for junctions via segment mapping
[2018-10-12 22:51:18] Retrieving sequences for splices
[2018-10-12 22:53:17] Indexing splices
[2018-10-12 22:53:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:53:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:53:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:53:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:53:55] Joining segment hits
[2018-10-12 22:56:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:56:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:56:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:56:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:56:25] Joining segment hits
[2018-10-12 22:58:36] Reporting output tracks
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[2018-10-12 23:02:17] A summary of the alignment counts can be found in /scratch/8792803.1.linga/tophat2/align_summary.txt
[2018-10-12 23:02:17] Run complete: 00:26:51 elapsed