[2018-10-13 01:40:44] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:40:44] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:40:44] Checking for Bowtie index files (genome)..
[2018-10-13 01:40:44] Checking for reference FASTA file
[2018-10-13 01:40:44] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:40:46] Reading known junctions from GTF file
[2018-10-13 01:40:49] Preparing reads
	 left reads: min. length=100, max. length=100, 1165736 kept reads (659 discarded)
	right reads: min. length=100, max. length=100, 1164811 kept reads (1584 discarded)
[2018-10-13 01:41:23] Building transcriptome data files /scratch/8792892.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:41:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:46:25] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:47:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:48:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:48:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:48:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:48:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:49:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:49:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:49:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:50:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:50:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:50:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:50:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:50:39] Searching for junctions via segment mapping
[2018-10-13 01:52:19] Retrieving sequences for splices
[2018-10-13 01:53:26] Indexing splices
[2018-10-13 01:53:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:53:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:53:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:53:46] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:53:48] Joining segment hits
[2018-10-13 01:55:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:55:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:55:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:55:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:55:18] Joining segment hits
[2018-10-13 01:56:36] Reporting output tracks
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[2018-10-13 01:59:38] A summary of the alignment counts can be found in /scratch/8792892.1.p8/tophat2/align_summary.txt
[2018-10-13 01:59:38] Run complete: 00:18:53 elapsed