[2018-10-13 02:58:14] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:58:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:58:15] Checking for Bowtie index files (genome)..
[2018-10-13 02:58:15] Checking for reference FASTA file
[2018-10-13 02:58:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:58:16] Reading known junctions from GTF file
[2018-10-13 02:58:19] Preparing reads
	 left reads: min. length=100, max. length=100, 387292 kept reads (335 discarded)
	right reads: min. length=100, max. length=100, 386980 kept reads (647 discarded)
[2018-10-13 02:58:30] Building transcriptome data files /scratch/8792939.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:58:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:03:21] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:03:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:04:08] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:04:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:04:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:04:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:04:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:04:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:04:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:05:17] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:05:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:05:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:05:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:05:37] Searching for junctions via segment mapping
[2018-10-13 03:07:00] Retrieving sequences for splices
[2018-10-13 03:08:07] Indexing splices
[2018-10-13 03:08:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:08:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:08:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:08:24] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:08:26] Joining segment hits
[2018-10-13 03:09:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:09:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:09:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:09:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:09:52] Joining segment hits
[2018-10-13 03:11:09] Reporting output tracks
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[2018-10-13 03:13:02] A summary of the alignment counts can be found in /scratch/8792939.1.p16/tophat2/align_summary.txt
[2018-10-13 03:13:02] Run complete: 00:14:47 elapsed