[2018-10-13 18:01:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:01:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:01:41] Checking for Bowtie index files (genome)..
[2018-10-13 18:01:41] Checking for reference FASTA file
[2018-10-13 18:01:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:01:45] Reading known junctions from GTF file
[2018-10-13 18:01:51] Preparing reads
	 left reads: min. length=100, max. length=100, 481472 kept reads (281 discarded)
	right reads: min. length=100, max. length=100, 481144 kept reads (609 discarded)
[2018-10-13 18:02:17] Building transcriptome data files /scratch/8793422.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:02:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:11:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:12:26] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:13:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:14:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:14:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:14:25] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:14:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:14:48] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:15:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:15:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:15:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:16:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:16:22] Searching for junctions via segment mapping
[2018-10-13 18:19:21] Retrieving sequences for splices
[2018-10-13 18:21:46] Indexing splices
[2018-10-13 18:22:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:22:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:22:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:22:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:22:28] Joining segment hits
[2018-10-13 18:25:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:25:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:25:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:25:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:25:25] Joining segment hits
[2018-10-13 18:28:04] Reporting output tracks
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[2018-10-13 18:32:05] A summary of the alignment counts can be found in /scratch/8793422.1.linga/tophat2/align_summary.txt
[2018-10-13 18:32:05] Run complete: 00:30:24 elapsed