[2019-06-18 11:07:54] Beginning TopHat run (v2.1.1)
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[2019-06-18 11:07:54] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-18 11:07:54] Checking for Bowtie index files (genome)..
[2019-06-18 11:07:54] Checking for reference FASTA file
[2019-06-18 11:07:54] Generating SAM header for Bowtie2Index/genome
[2019-06-18 11:07:59] Reading known junctions from GTF file
[2019-06-18 11:08:03] Preparing reads
	 left reads: min. length=50, max. length=50, 57146761 kept reads (91217 discarded)
	right reads: min. length=50, max. length=50, 56982350 kept reads (255628 discarded)
[2019-06-18 11:34:40] Building transcriptome data files /scratch/6794465.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-18 11:35:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-18 11:41:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 11:57:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-18 12:12:59] Resuming TopHat pipeline with unmapped reads
[2019-06-18 12:13:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 12:39:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 12:42:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 12:48:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-18 13:16:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-18 13:20:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-18 13:27:55] Searching for junctions via segment mapping
[2019-06-18 13:37:40] Retrieving sequences for splices
[2019-06-18 13:40:21] Indexing splices
[2019-06-18 13:40:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 13:41:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 13:41:51] Joining segment hits
[2019-06-18 13:45:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-18 13:46:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-18 13:47:26] Joining segment hits
[2019-06-18 13:51:36] Reporting output tracks
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[2019-06-18 14:57:20] A summary of the alignment counts can be found in /scratch/6794465.1.linga/tophat2/align_summary.txt
[2019-06-18 14:57:20] Run complete: 03:49:26 elapsed