[2018-10-13 00:47:22] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:47:22] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:47:22] Checking for Bowtie index files (genome)..
[2018-10-13 00:47:22] Checking for reference FASTA file
[2018-10-13 00:47:22] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:47:24] Reading known junctions from GTF file
[2018-10-13 00:47:27] Preparing reads
	 left reads: min. length=100, max. length=100, 341838 kept reads (167 discarded)
	right reads: min. length=100, max. length=100, 341519 kept reads (486 discarded)
[2018-10-13 00:47:37] Building transcriptome data files /scratch/8792871.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:47:48] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:53:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:54:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:54:22] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:54:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:54:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:54:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:54:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:55:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:55:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:55:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:55:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:55:40] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:55:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:55:51] Searching for junctions via segment mapping
[2018-10-13 00:57:16] Retrieving sequences for splices
[2018-10-13 00:58:28] Indexing splices
[2018-10-13 00:58:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:58:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:58:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:58:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:58:51] Joining segment hits
[2018-10-13 01:00:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:00:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:00:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:00:13] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:00:15] Joining segment hits
[2018-10-13 01:01:31] Reporting output tracks
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[2018-10-13 01:03:22] A summary of the alignment counts can be found in /scratch/8792871.1.c/tophat2/align_summary.txt
[2018-10-13 01:03:22] Run complete: 00:15:59 elapsed