[2018-10-13 10:51:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:51:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:51:29] Checking for Bowtie index files (genome)..
[2018-10-13 10:51:29] Checking for reference FASTA file
[2018-10-13 10:51:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:51:31] Reading known junctions from GTF file
[2018-10-13 10:51:33] Preparing reads
	 left reads: min. length=100, max. length=100, 937280 kept reads (150 discarded)
	right reads: min. length=100, max. length=100, 936946 kept reads (484 discarded)
[2018-10-13 10:52:00] Building transcriptome data files /scratch/8793188.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:52:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:56:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:57:35] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:58:13] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:58:13] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:58:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:58:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:58:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:58:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:58:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:59:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:59:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:59:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:59:31] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:59:37] Searching for junctions via segment mapping
[2018-10-13 11:02:19] Retrieving sequences for splices
[2018-10-13 11:03:26] Indexing splices
[2018-10-13 11:03:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:03:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:03:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:03:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:03:52] Joining segment hits
[2018-10-13 11:05:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:05:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:05:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:05:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:05:22] Joining segment hits
[2018-10-13 11:06:37] Reporting output tracks
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[2018-10-13 11:14:37] A summary of the alignment counts can be found in /scratch/8793188.1.p8/tophat2/align_summary.txt
[2018-10-13 11:14:37] Run complete: 00:23:07 elapsed