[2018-10-13 04:43:55] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:43:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:43:55] Checking for Bowtie index files (genome)..
[2018-10-13 04:43:55] Checking for reference FASTA file
[2018-10-13 04:43:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:43:57] Reading known junctions from GTF file
[2018-10-13 04:43:59] Preparing reads
	 left reads: min. length=100, max. length=100, 808349 kept reads (69 discarded)
	right reads: min. length=100, max. length=100, 808042 kept reads (376 discarded)
[2018-10-13 04:44:22] Building transcriptome data files /scratch/8792999.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:44:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:49:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:49:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:50:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:50:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:50:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:50:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:50:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:50:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:50:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:50:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:50:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:51:04] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:51:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:51:14] Searching for junctions via segment mapping
[2018-10-13 04:53:03] Retrieving sequences for splices
[2018-10-13 04:54:10] Indexing splices
[2018-10-13 04:54:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:54:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:54:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:54:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:54:32] Joining segment hits
[2018-10-13 04:55:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:55:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:55:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:55:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:55:57] Joining segment hits
[2018-10-13 04:57:12] Reporting output tracks
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[2018-10-13 05:01:15] A summary of the alignment counts can be found in /scratch/8792999.1.p8/tophat2/align_summary.txt
[2018-10-13 05:01:15] Run complete: 00:17:19 elapsed