[2018-10-13 03:35:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:35:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:35:51] Checking for Bowtie index files (genome)..
[2018-10-13 03:35:51] Checking for reference FASTA file
[2018-10-13 03:35:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:35:53] Reading known junctions from GTF file
[2018-10-13 03:35:56] Preparing reads
	 left reads: min. length=100, max. length=100, 447928 kept reads (272 discarded)
	right reads: min. length=100, max. length=100, 447805 kept reads (395 discarded)
[2018-10-13 03:36:08] Building transcriptome data files /scratch/8792963.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:36:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:41:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:41:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:41:55] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:41:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:42:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:42:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:42:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:42:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:42:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:42:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:42:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:42:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:42:57] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:43:03] Searching for junctions via segment mapping
[2018-10-13 03:45:14] Retrieving sequences for splices
[2018-10-13 03:46:21] Indexing splices
[2018-10-13 03:46:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:46:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:46:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:46:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:46:44] Joining segment hits
[2018-10-13 03:47:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:48:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:48:04] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:48:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:48:09] Joining segment hits
[2018-10-13 03:49:24] Reporting output tracks
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[2018-10-13 03:54:21] A summary of the alignment counts can be found in /scratch/8792963.1.p16/tophat2/align_summary.txt
[2018-10-13 03:54:21] Run complete: 00:18:30 elapsed