[2018-10-13 08:43:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:43:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:43:40] Checking for Bowtie index files (genome)..
[2018-10-13 08:43:40] Checking for reference FASTA file
[2018-10-13 08:43:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:43:42] Reading known junctions from GTF file
[2018-10-13 08:43:44] Preparing reads
	 left reads: min. length=100, max. length=100, 577775 kept reads (115 discarded)
	right reads: min. length=100, max. length=100, 577650 kept reads (240 discarded)
[2018-10-13 08:44:00] Building transcriptome data files /scratch/8793125.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:44:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:48:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:49:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:50:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:50:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:50:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:50:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:50:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:50:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:50:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:50:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:51:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:51:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:51:12] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:51:17] Searching for junctions via segment mapping
[2018-10-13 08:54:20] Retrieving sequences for splices
[2018-10-13 08:55:27] Indexing splices
[2018-10-13 08:55:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:55:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:55:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:55:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:55:54] Joining segment hits
[2018-10-13 08:57:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:57:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:57:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:57:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:57:24] Joining segment hits
[2018-10-13 08:58:40] Reporting output tracks
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[2018-10-13 09:07:21] A summary of the alignment counts can be found in /scratch/8793125.1.p16/tophat2/align_summary.txt
[2018-10-13 09:07:21] Run complete: 00:23:40 elapsed