[2018-10-13 13:37:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:37:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:37:34] Checking for Bowtie index files (genome)..
[2018-10-13 13:37:34] Checking for reference FASTA file
[2018-10-13 13:37:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:37:36] Reading known junctions from GTF file
[2018-10-13 13:37:39] Preparing reads
	 left reads: min. length=100, max. length=100, 1005039 kept reads (193 discarded)
	right reads: min. length=100, max. length=100, 1004831 kept reads (401 discarded)
[2018-10-13 13:38:05] Building transcriptome data files /scratch/8793267.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:38:15] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:42:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:43:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:44:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:44:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:44:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:44:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:45:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:45:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:45:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:45:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:45:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:46:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:46:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:46:18] Searching for junctions via segment mapping
[2018-10-13 13:50:04] Retrieving sequences for splices
[2018-10-13 13:51:10] Indexing splices
[2018-10-13 13:51:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:51:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:51:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:51:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:51:40] Joining segment hits
[2018-10-13 13:52:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:53:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:53:06] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:53:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:53:14] Joining segment hits
[2018-10-13 13:54:31] Reporting output tracks
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[2018-10-13 14:01:46] A summary of the alignment counts can be found in /scratch/8793267.1.p16/tophat2/align_summary.txt
[2018-10-13 14:01:46] Run complete: 00:24:11 elapsed