[2019-06-26 14:44:08] Beginning TopHat run (v2.1.1)
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[2019-06-26 14:44:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 14:44:08] Checking for Bowtie index files (genome)..
[2019-06-26 14:44:08] Checking for reference FASTA file
[2019-06-26 14:44:08] Generating SAM header for Bowtie2Index/genome
[2019-06-26 14:44:13] Reading known junctions from GTF file
[2019-06-26 14:44:18] Preparing reads
	 left reads: min. length=35, max. length=76, 25494098 kept reads (863853 discarded)
	right reads: min. length=35, max. length=76, 26194098 kept reads (163853 discarded)
[2019-06-26 15:02:52] Building transcriptome data files /scratch/7076169.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 15:03:11] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 15:11:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 15:29:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 15:55:05] Resuming TopHat pipeline with unmapped reads
[2019-06-26 15:55:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 16:07:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 16:10:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 16:13:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 16:15:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 16:32:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 16:38:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 16:43:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 16:48:39] Searching for junctions via segment mapping
[2019-06-26 17:01:55] Retrieving sequences for splices
[2019-06-26 17:04:40] Indexing splices
[2019-06-26 17:05:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 17:05:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 17:06:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 17:07:55] Joining segment hits
[2019-06-26 17:12:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 17:13:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 17:15:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 17:18:47] Joining segment hits
[2019-06-26 17:24:45] Reporting output tracks
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[2019-06-26 23:02:03] A summary of the alignment counts can be found in /scratch/7076169.1.linga/tophat2/align_summary.txt
[2019-06-26 23:02:03] Run complete: 08:17:54 elapsed