[2018-10-13 00:31:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:31:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:31:16] Checking for Bowtie index files (genome)..
[2018-10-13 00:31:16] Checking for reference FASTA file
[2018-10-13 00:31:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:31:18] Reading known junctions from GTF file
[2018-10-13 00:31:20] Preparing reads
	 left reads: min. length=100, max. length=100, 378897 kept reads (138 discarded)
	right reads: min. length=100, max. length=100, 378533 kept reads (502 discarded)
[2018-10-13 00:31:32] Building transcriptome data files /scratch/8792866.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:31:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:36:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:37:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:37:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:37:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:37:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:37:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:37:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:38:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:38:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:38:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:38:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:38:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:38:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:38:51] Searching for junctions via segment mapping
[2018-10-13 00:40:11] Retrieving sequences for splices
[2018-10-13 00:41:18] Indexing splices
[2018-10-13 00:41:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:41:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:41:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:41:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:41:38] Joining segment hits
[2018-10-13 00:42:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:43:00] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:43:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:43:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:43:07] Joining segment hits
[2018-10-13 00:44:26] Reporting output tracks
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[2018-10-13 00:46:21] A summary of the alignment counts can be found in /scratch/8792866.1.p8/tophat2/align_summary.txt
[2018-10-13 00:46:21] Run complete: 00:15:05 elapsed