[2018-10-13 08:12:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:12:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:12:30] Checking for Bowtie index files (genome)..
[2018-10-13 08:12:30] Checking for reference FASTA file
[2018-10-13 08:12:30] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:12:32] Reading known junctions from GTF file
[2018-10-13 08:12:34] Preparing reads
	 left reads: min. length=100, max. length=100, 1382378 kept reads (139 discarded)
	right reads: min. length=100, max. length=100, 1381971 kept reads (546 discarded)
[2018-10-13 08:13:12] Building transcriptome data files /scratch/8793108.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:13:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:18:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:19:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:20:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:20:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:20:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:20:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:21:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:21:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:21:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:21:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:21:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:22:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:22:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:22:23] Searching for junctions via segment mapping
[2018-10-13 08:26:07] Retrieving sequences for splices
[2018-10-13 08:27:14] Indexing splices
[2018-10-13 08:27:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:27:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:27:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:27:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:27:44] Joining segment hits
[2018-10-13 08:29:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:29:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:29:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:29:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:29:20] Joining segment hits
[2018-10-13 08:30:38] Reporting output tracks
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[2018-10-13 08:39:56] A summary of the alignment counts can be found in /scratch/8793108.1.p16/tophat2/align_summary.txt
[2018-10-13 08:39:56] Run complete: 00:27:26 elapsed