[2018-10-13 03:13:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:13:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:13:10] Checking for Bowtie index files (genome)..
[2018-10-13 03:13:10] Checking for reference FASTA file
[2018-10-13 03:13:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:13:15] Reading known junctions from GTF file
[2018-10-13 03:13:19] Preparing reads
	 left reads: min. length=100, max. length=100, 342874 kept reads (66 discarded)
	right reads: min. length=100, max. length=100, 342730 kept reads (210 discarded)
[2018-10-13 03:13:34] Building transcriptome data files /scratch/8792945.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:13:54] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:22:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:23:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:23:51] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:23:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:24:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:24:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:24:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:24:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:25:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:25:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:25:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:25:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:26:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:26:17] Searching for junctions via segment mapping
[2018-10-13 03:28:58] Retrieving sequences for splices
[2018-10-13 03:31:07] Indexing splices
[2018-10-13 03:31:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:31:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:31:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:31:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:31:45] Joining segment hits
[2018-10-13 03:34:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:34:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:34:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:34:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:34:21] Joining segment hits
[2018-10-13 03:37:10] Reporting output tracks
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[2018-10-13 03:40:35] A summary of the alignment counts can be found in /scratch/8792945.1.linga/tophat2/align_summary.txt
[2018-10-13 03:40:35] Run complete: 00:27:24 elapsed