[2019-06-18 11:07:59] Beginning TopHat run (v2.1.1)
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[2019-06-18 11:07:59] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-18 11:07:59] Checking for Bowtie index files (genome)..
[2019-06-18 11:07:59] Checking for reference FASTA file
[2019-06-18 11:07:59] Generating SAM header for Bowtie2Index/genome
[2019-06-18 11:08:05] Reading known junctions from GTF file
[2019-06-18 11:08:09] Preparing reads
	 left reads: min. length=50, max. length=50, 59318772 kept reads (89948 discarded)
	right reads: min. length=50, max. length=50, 59151287 kept reads (257433 discarded)
[2019-06-18 11:38:40] Building transcriptome data files /scratch/6794463.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-18 11:38:59] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-18 11:46:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:02:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:18:51] Resuming TopHat pipeline with unmapped reads
[2019-06-18 12:18:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 12:42:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 12:45:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 12:50:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 13:16:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 13:21:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:27:10] Searching for junctions via segment mapping
[2019-06-18 13:35:52] Retrieving sequences for splices
[2019-06-18 13:38:34] Indexing splices
[2019-06-18 13:39:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 13:39:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 13:40:14] Joining segment hits
[2019-06-18 13:44:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 13:44:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 13:45:19] Joining segment hits
[2019-06-18 13:49:22] Reporting output tracks
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[2019-06-18 14:53:06] A summary of the alignment counts can be found in /scratch/6794463.1.linga/tophat2/align_summary.txt
[2019-06-18 14:53:06] Run complete: 03:45:07 elapsed