[2018-10-13 05:53:20] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:53:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:53:20] Checking for Bowtie index files (genome)..
[2018-10-13 05:53:20] Checking for reference FASTA file
[2018-10-13 05:53:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:53:24] Reading known junctions from GTF file
[2018-10-13 05:53:28] Preparing reads
	 left reads: min. length=100, max. length=100, 1189074 kept reads (86 discarded)
	right reads: min. length=100, max. length=100, 1188699 kept reads (461 discarded)
[2018-10-13 05:54:16] Building transcriptome data files /scratch/8793035.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:54:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:02:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:03:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:04:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:04:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:05:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:05:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:05:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:05:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:05:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:06:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:06:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:06:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:06:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:07:09] Searching for junctions via segment mapping
[2018-10-13 06:11:06] Retrieving sequences for splices
[2018-10-13 06:13:06] Indexing splices
[2018-10-13 06:13:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:13:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:13:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:13:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:13:53] Joining segment hits
[2018-10-13 06:16:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:16:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:16:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:16:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:16:37] Joining segment hits
[2018-10-13 06:19:00] Reporting output tracks
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[2018-10-13 06:28:39] A summary of the alignment counts can be found in /scratch/8793035.1.linga/tophat2/align_summary.txt
[2018-10-13 06:28:39] Run complete: 00:35:19 elapsed