[2019-05-08 08:23:54] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:23:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:23:55] Checking for Bowtie index files (genome)..
[2019-05-08 08:23:55] Checking for reference FASTA file
[2019-05-08 08:23:55] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:23:57] Reading known junctions from GTF file
[2019-05-08 08:23:59] Preparing reads
	 left reads: min. length=101, max. length=101, 34965568 kept reads (210218 discarded)
[2019-05-08 08:33:14] Building transcriptome data files /scratch/5992722.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:33:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:38:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 08:48:11] Resuming TopHat pipeline with unmapped reads
[2019-05-08 08:48:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 08:55:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 08:56:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 08:56:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 08:57:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 08:58:32] Searching for junctions via segment mapping
[2019-05-08 09:01:04] Retrieving sequences for splices
[2019-05-08 09:02:11] Indexing splices
[2019-05-08 09:02:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:02:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:02:56] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:03:08] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:03:20] Joining segment hits
[2019-05-08 09:05:00] Reporting output tracks
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[2019-05-08 09:16:18] A summary of the alignment counts can be found in /scratch/5992722.1.p16/tophat2/align_summary.txt
[2019-05-08 09:16:18] Run complete: 00:52:23 elapsed