[2018-10-13 09:05:55] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:05:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:05:55] Checking for Bowtie index files (genome)..
[2018-10-13 09:05:55] Checking for reference FASTA file
[2018-10-13 09:05:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:06:00] Reading known junctions from GTF file
[2018-10-13 09:06:04] Preparing reads
	 left reads: min. length=100, max. length=100, 960782 kept reads (146 discarded)
	right reads: min. length=100, max. length=100, 960538 kept reads (390 discarded)
[2018-10-13 09:06:47] Building transcriptome data files /scratch/8793134.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:07:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:15:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:16:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:17:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:17:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:17:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:18:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:18:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:18:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:18:34] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:19:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:19:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:19:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:19:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:19:55] Searching for junctions via segment mapping
[2018-10-13 09:23:49] Retrieving sequences for splices
[2018-10-13 09:25:58] Indexing splices
[2018-10-13 09:26:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:26:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:26:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:26:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:26:46] Joining segment hits
[2018-10-13 09:29:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:29:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:29:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:29:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:29:36] Joining segment hits
[2018-10-13 09:32:20] Reporting output tracks
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[2018-10-13 09:40:00] A summary of the alignment counts can be found in /scratch/8793134.1.linga/tophat2/align_summary.txt
[2018-10-13 09:40:00] Run complete: 00:34:05 elapsed