[2018-10-13 17:59:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:59:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:59:51] Checking for Bowtie index files (genome)..
[2018-10-13 17:59:51] Checking for reference FASTA file
[2018-10-13 17:59:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:59:53] Reading known junctions from GTF file
[2018-10-13 17:59:56] Preparing reads
	 left reads: min. length=100, max. length=100, 281617 kept reads (145 discarded)
	right reads: min. length=100, max. length=100, 281332 kept reads (430 discarded)
[2018-10-13 18:00:04] Building transcriptome data files /scratch/8793421.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:00:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:04:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:05:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:05:27] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:05:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:05:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:05:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:05:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:05:56] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:06:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:06:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:06:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:06:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:06:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:06:34] Searching for junctions via segment mapping
[2018-10-13 18:07:52] Retrieving sequences for splices
[2018-10-13 18:08:58] Indexing splices
[2018-10-13 18:09:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:09:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:09:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:09:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:09:18] Joining segment hits
[2018-10-13 18:10:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:10:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:10:38] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:10:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:10:42] Joining segment hits
[2018-10-13 18:11:56] Reporting output tracks
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[2018-10-13 18:13:33] A summary of the alignment counts can be found in /scratch/8793421.1.p16/tophat2/align_summary.txt
[2018-10-13 18:13:33] Run complete: 00:13:41 elapsed