[2018-10-13 01:09:47] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:09:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:09:47] Checking for Bowtie index files (genome)..
[2018-10-13 01:09:47] Checking for reference FASTA file
[2018-10-13 01:09:47] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:09:49] Reading known junctions from GTF file
[2018-10-13 01:09:52] Preparing reads
	 left reads: min. length=100, max. length=100, 512834 kept reads (262 discarded)
	right reads: min. length=100, max. length=100, 512472 kept reads (624 discarded)
[2018-10-13 01:10:07] Building transcriptome data files /scratch/8792878.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:10:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:15:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:16:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:16:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:16:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:17:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:17:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:17:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:17:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:17:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:17:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:18:02] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:18:10] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:18:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:18:22] Searching for junctions via segment mapping
[2018-10-13 01:19:55] Retrieving sequences for splices
[2018-10-13 01:21:08] Indexing splices
[2018-10-13 01:21:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:21:23] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:21:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:21:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:21:30] Joining segment hits
[2018-10-13 01:22:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:22:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:22:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:22:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:22:58] Joining segment hits
[2018-10-13 01:24:16] Reporting output tracks
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[2018-10-13 01:26:34] A summary of the alignment counts can be found in /scratch/8792878.1.c/tophat2/align_summary.txt
[2018-10-13 01:26:34] Run complete: 00:16:46 elapsed