[2018-10-13 03:22:51] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:22:51] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:22:51] Checking for Bowtie index files (genome)..
[2018-10-13 03:22:51] Checking for reference FASTA file
[2018-10-13 03:22:51] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:22:53] Reading known junctions from GTF file
[2018-10-13 03:22:56] Preparing reads
	 left reads: min. length=100, max. length=100, 246811 kept reads (234 discarded)
	right reads: min. length=100, max. length=100, 246540 kept reads (505 discarded)
[2018-10-13 03:23:03] Building transcriptome data files /scratch/8792956.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:23:13] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:29:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:29:22] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:29:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:29:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:30:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:30:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:30:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:30:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:30:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:30:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:30:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:30:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:30:57] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:31:02] Searching for junctions via segment mapping
[2018-10-13 03:32:23] Retrieving sequences for splices
[2018-10-13 03:33:36] Indexing splices
[2018-10-13 03:33:46] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:33:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:33:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:33:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:33:55] Joining segment hits
[2018-10-13 03:35:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:35:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:35:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:35:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:35:20] Joining segment hits
[2018-10-13 03:36:36] Reporting output tracks
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[2018-10-13 03:38:10] A summary of the alignment counts can be found in /scratch/8792956.1.c/tophat2/align_summary.txt
[2018-10-13 03:38:10] Run complete: 00:15:18 elapsed