[2018-10-13 17:03:11] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:03:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:03:11] Checking for Bowtie index files (genome)..
[2018-10-13 17:03:11] Checking for reference FASTA file
[2018-10-13 17:03:11] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:03:15] Reading known junctions from GTF file
[2018-10-13 17:03:19] Preparing reads
	 left reads: min. length=100, max. length=100, 250533 kept reads (146 discarded)
	right reads: min. length=100, max. length=100, 250382 kept reads (297 discarded)
[2018-10-13 17:03:30] Building transcriptome data files /scratch/8793383.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:03:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:12:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:12:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:13:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:13:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:13:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:13:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:13:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:14:05] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:14:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:14:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:14:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:14:37] Searching for junctions via segment mapping
[2018-10-13 17:17:02] Retrieving sequences for splices
[2018-10-13 17:19:08] Indexing splices
[2018-10-13 17:19:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:19:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:19:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:19:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:19:45] Joining segment hits
[2018-10-13 17:21:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:21:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:22:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:22:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:22:10] Joining segment hits
[2018-10-13 17:24:29] Reporting output tracks
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[2018-10-13 17:27:24] A summary of the alignment counts can be found in /scratch/8793383.1.linga/tophat2/align_summary.txt
[2018-10-13 17:27:24] Run complete: 00:24:12 elapsed