[2018-10-13 05:22:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:22:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:22:09] Checking for Bowtie index files (genome)..
[2018-10-13 05:22:09] Checking for reference FASTA file
[2018-10-13 05:22:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:22:11] Reading known junctions from GTF file
[2018-10-13 05:22:13] Preparing reads
	 left reads: min. length=100, max. length=100, 924062 kept reads (115 discarded)
	right reads: min. length=100, max. length=100, 923873 kept reads (304 discarded)
[2018-10-13 05:22:39] Building transcriptome data files /scratch/8793023.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:22:51] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:27:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:28:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:28:30] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:28:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:28:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:28:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:28:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:29:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:29:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:29:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:29:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:29:34] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:29:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:29:45] Searching for junctions via segment mapping
[2018-10-13 05:31:57] Retrieving sequences for splices
[2018-10-13 05:33:04] Indexing splices
[2018-10-13 05:33:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:33:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:33:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:33:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:33:26] Joining segment hits
[2018-10-13 05:34:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:34:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:34:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:34:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:34:52] Joining segment hits
[2018-10-13 05:36:08] Reporting output tracks
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[2018-10-13 05:41:09] A summary of the alignment counts can be found in /scratch/8793023.1.p16/tophat2/align_summary.txt
[2018-10-13 05:41:09] Run complete: 00:19:00 elapsed