[2018-10-13 14:28:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:28:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:28:51] Checking for Bowtie index files (genome)..
[2018-10-13 14:28:51] Checking for reference FASTA file
[2018-10-13 14:28:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:28:53] Reading known junctions from GTF file
[2018-10-13 14:28:55] Preparing reads
	 left reads: min. length=100, max. length=100, 230968 kept reads (121 discarded)
	right reads: min. length=100, max. length=100, 230798 kept reads (291 discarded)
[2018-10-13 14:29:02] Building transcriptome data files /scratch/8793291.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:29:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:33:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:34:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:34:25] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:34:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:34:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:34:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:34:49] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:34:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:34:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:35:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:35:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:35:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:35:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:35:31] Searching for junctions via segment mapping
[2018-10-13 14:36:48] Retrieving sequences for splices
[2018-10-13 14:37:55] Indexing splices
[2018-10-13 14:38:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:38:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:38:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:38:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:38:16] Joining segment hits
[2018-10-13 14:39:25] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:39:27] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:39:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:39:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:39:34] Joining segment hits
[2018-10-13 14:40:43] Reporting output tracks
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[2018-10-13 14:42:15] A summary of the alignment counts can be found in /scratch/8793291.1.p16/tophat2/align_summary.txt
[2018-10-13 14:42:15] Run complete: 00:13:23 elapsed