[2018-10-13 01:42:52] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:42:52] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:42:52] Checking for Bowtie index files (genome)..
[2018-10-13 01:42:52] Checking for reference FASTA file
[2018-10-13 01:42:52] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:42:54] Reading known junctions from GTF file
[2018-10-13 01:42:56] Preparing reads
	 left reads: min. length=100, max. length=100, 710699 kept reads (444 discarded)
	right reads: min. length=100, max. length=100, 710058 kept reads (1085 discarded)
[2018-10-13 01:43:16] Building transcriptome data files /scratch/8792894.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:43:26] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:48:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:48:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:49:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:49:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:49:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:49:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:50:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:50:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:50:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:50:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:50:50] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:50:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:51:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:51:10] Searching for junctions via segment mapping
[2018-10-13 01:52:54] Retrieving sequences for splices
[2018-10-13 01:54:01] Indexing splices
[2018-10-13 01:54:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:54:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:54:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:54:19] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:54:22] Joining segment hits
[2018-10-13 01:55:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:55:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:55:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:55:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:55:49] Joining segment hits
[2018-10-13 01:57:05] Reporting output tracks
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[2018-10-13 01:59:55] A summary of the alignment counts can be found in /scratch/8792894.1.p16/tophat2/align_summary.txt
[2018-10-13 01:59:55] Run complete: 00:17:03 elapsed