[2019-04-29 17:29:57] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:29:57] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:29:57] Checking for Bowtie index files (genome)..
[2019-04-29 17:29:57] Checking for reference FASTA file
[2019-04-29 17:29:57] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:29:59] Reading known junctions from GTF file
[2019-04-29 17:30:01] Preparing reads
	 left reads: min. length=50, max. length=50, 65460204 kept reads (20232 discarded)
	right reads: min. length=50, max. length=50, 65434499 kept reads (45937 discarded)
[2019-04-29 17:51:13] Building transcriptome data files /scratch/5765365.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:51:22] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:56:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:12:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:27:38] Resuming TopHat pipeline with unmapped reads
[2019-04-29 18:27:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 18:34:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 18:35:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 18:36:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 18:44:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 18:46:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 18:49:31] Searching for junctions via segment mapping
[2019-04-29 18:54:04] Retrieving sequences for splices
[2019-04-29 18:55:04] Indexing splices
[2019-04-29 18:55:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 18:55:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 18:55:59] Joining segment hits
[2019-04-29 18:57:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 18:57:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 18:58:17] Joining segment hits
[2019-04-29 18:59:45] Reporting output tracks
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[2019-04-29 19:42:08] A summary of the alignment counts can be found in /scratch/5765365.1.p/tophat2/align_summary.txt
[2019-04-29 19:42:08] Run complete: 02:12:11 elapsed