[2018-10-13 09:48:35] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:48:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:48:35] Checking for Bowtie index files (genome)..
[2018-10-13 09:48:35] Checking for reference FASTA file
[2018-10-13 09:48:35] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:48:40] Reading known junctions from GTF file
[2018-10-13 09:48:44] Preparing reads
	 left reads: min. length=100, max. length=100, 1037371 kept reads (111 discarded)
	right reads: min. length=100, max. length=100, 1037024 kept reads (458 discarded)
[2018-10-13 09:49:25] Building transcriptome data files /scratch/8793156.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:49:45] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:57:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:58:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:59:20] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:59:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:00:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:00:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:00:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:00:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:00:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:01:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:01:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:01:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:02:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:02:13] Searching for junctions via segment mapping
[2018-10-13 10:06:13] Retrieving sequences for splices
[2018-10-13 10:08:18] Indexing splices
[2018-10-13 10:08:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:08:45] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:08:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:08:58] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:09:05] Joining segment hits
[2018-10-13 10:11:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:11:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:11:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:11:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:12:00] Joining segment hits
[2018-10-13 10:14:21] Reporting output tracks
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[2018-10-13 10:25:19] A summary of the alignment counts can be found in /scratch/8793156.1.linga/tophat2/align_summary.txt
[2018-10-13 10:25:19] Run complete: 00:36:44 elapsed