[2018-10-13 07:37:00] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:37:00] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:37:00] Checking for Bowtie index files (genome)..
[2018-10-13 07:37:00] Checking for reference FASTA file
[2018-10-13 07:37:00] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:37:02] Reading known junctions from GTF file
[2018-10-13 07:37:04] Preparing reads
	 left reads: min. length=100, max. length=100, 674362 kept reads (97 discarded)
	right reads: min. length=100, max. length=100, 674173 kept reads (286 discarded)
[2018-10-13 07:37:24] Building transcriptome data files /scratch/8793091.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:37:34] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:42:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:42:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:43:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:43:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:43:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:43:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:43:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:43:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:43:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:44:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:44:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:44:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:44:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:44:22] Searching for junctions via segment mapping
[2018-10-13 07:46:32] Retrieving sequences for splices
[2018-10-13 07:47:40] Indexing splices
[2018-10-13 07:47:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:47:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:47:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:48:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:48:04] Joining segment hits
[2018-10-13 07:49:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:49:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:49:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:49:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:49:31] Joining segment hits
[2018-10-13 07:50:46] Reporting output tracks
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[2018-10-13 07:56:07] A summary of the alignment counts can be found in /scratch/8793091.1.p16/tophat2/align_summary.txt
[2018-10-13 07:56:07] Run complete: 00:19:07 elapsed