[2018-10-13 15:56:20] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:56:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:56:20] Checking for Bowtie index files (genome)..
[2018-10-13 15:56:20] Checking for reference FASTA file
[2018-10-13 15:56:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:56:22] Reading known junctions from GTF file
[2018-10-13 15:56:24] Preparing reads
	 left reads: min. length=100, max. length=100, 260659 kept reads (172 discarded)
	right reads: min. length=100, max. length=100, 260521 kept reads (310 discarded)
[2018-10-13 15:56:32] Building transcriptome data files /scratch/8793338.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:56:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:01:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:01:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:01:51] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:01:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:02:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:02:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:02:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:02:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:02:19] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:02:31] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:02:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:02:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:02:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:02:48] Searching for junctions via segment mapping
[2018-10-13 16:04:06] Retrieving sequences for splices
[2018-10-13 16:05:13] Indexing splices
[2018-10-13 16:05:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:05:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:05:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:05:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:05:32] Joining segment hits
[2018-10-13 16:06:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:06:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:06:45] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:06:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:06:49] Joining segment hits
[2018-10-13 16:07:58] Reporting output tracks
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[2018-10-13 16:09:31] A summary of the alignment counts can be found in /scratch/8793338.1.p16/tophat2/align_summary.txt
[2018-10-13 16:09:31] Run complete: 00:13:11 elapsed