[2018-10-13 02:02:55] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:02:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:02:55] Checking for Bowtie index files (genome)..
[2018-10-13 02:02:55] Checking for reference FASTA file
[2018-10-13 02:02:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:02:59] Reading known junctions from GTF file
[2018-10-13 02:03:04] Preparing reads
	 left reads: min. length=100, max. length=100, 466526 kept reads (266 discarded)
	right reads: min. length=100, max. length=100, 466175 kept reads (617 discarded)
[2018-10-13 02:03:26] Building transcriptome data files /scratch/8792904.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:03:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:12:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:12:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:13:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:13:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:14:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:14:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:14:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:15:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:15:11] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:15:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:16:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:16:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:16:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:16:50] Searching for junctions via segment mapping
[2018-10-13 02:19:35] Retrieving sequences for splices
[2018-10-13 02:21:43] Indexing splices
[2018-10-13 02:22:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:22:07] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:22:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:22:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:22:20] Joining segment hits
[2018-10-13 02:25:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:25:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:25:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:25:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:25:41] Joining segment hits
[2018-10-13 02:28:02] Reporting output tracks
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[2018-10-13 02:31:53] A summary of the alignment counts can be found in /scratch/8792904.1.linga/tophat2/align_summary.txt
[2018-10-13 02:31:53] Run complete: 00:28:58 elapsed