[2018-10-13 05:33:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:33:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:33:34] Checking for Bowtie index files (genome)..
[2018-10-13 05:33:34] Checking for reference FASTA file
[2018-10-13 05:33:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:33:36] Reading known junctions from GTF file
[2018-10-13 05:33:38] Preparing reads
	 left reads: min. length=100, max. length=100, 823122 kept reads (170 discarded)
	right reads: min. length=100, max. length=100, 822971 kept reads (321 discarded)
[2018-10-13 05:33:58] Building transcriptome data files /scratch/8793029.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:34:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:38:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:39:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:39:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:39:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:39:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:40:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:40:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:40:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:40:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:40:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:40:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:40:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:40:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:40:49] Searching for junctions via segment mapping
[2018-10-13 05:42:42] Retrieving sequences for splices
[2018-10-13 05:43:49] Indexing splices
[2018-10-13 05:44:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:44:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:44:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:44:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:44:12] Joining segment hits
[2018-10-13 05:45:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:45:29] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:45:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:45:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:45:37] Joining segment hits
[2018-10-13 05:46:52] Reporting output tracks
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[2018-10-13 05:50:45] A summary of the alignment counts can be found in /scratch/8793029.1.p8/tophat2/align_summary.txt
[2018-10-13 05:50:45] Run complete: 00:17:11 elapsed