[2018-10-13 05:20:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:20:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:20:44] Checking for Bowtie index files (genome)..
[2018-10-13 05:20:44] Checking for reference FASTA file
[2018-10-13 05:20:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:20:49] Reading known junctions from GTF file
[2018-10-13 05:20:53] Preparing reads
	 left reads: min. length=100, max. length=100, 817966 kept reads (81 discarded)
	right reads: min. length=100, max. length=100, 817790 kept reads (257 discarded)
[2018-10-13 05:21:25] Building transcriptome data files /scratch/8793021.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:21:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:30:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:30:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:31:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:31:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:32:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:32:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:32:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:32:39] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:32:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:33:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:33:31] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:33:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:33:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:34:06] Searching for junctions via segment mapping
[2018-10-13 05:37:22] Retrieving sequences for splices
[2018-10-13 05:39:25] Indexing splices
[2018-10-13 05:39:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:39:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:39:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:39:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:40:02] Joining segment hits
[2018-10-13 05:42:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:42:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:42:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:42:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:42:46] Joining segment hits
[2018-10-13 05:45:01] Reporting output tracks
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[2018-10-13 05:50:30] A summary of the alignment counts can be found in /scratch/8793021.1.linga/tophat2/align_summary.txt
[2018-10-13 05:50:30] Run complete: 00:29:46 elapsed