[2018-10-13 00:29:54] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:29:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:29:54] Checking for Bowtie index files (genome)..
[2018-10-13 00:29:54] Checking for reference FASTA file
[2018-10-13 00:29:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:29:56] Reading known junctions from GTF file
[2018-10-13 00:29:59] Preparing reads
	 left reads: min. length=100, max. length=100, 253478 kept reads (158 discarded)
	right reads: min. length=100, max. length=100, 253172 kept reads (464 discarded)
[2018-10-13 00:30:08] Building transcriptome data files /scratch/8792864.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:30:18] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:36:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:36:26] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:36:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:36:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:37:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:37:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:37:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:37:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:37:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:37:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:37:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:37:54] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:37:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:38:05] Searching for junctions via segment mapping
[2018-10-13 00:39:27] Retrieving sequences for splices
[2018-10-13 00:40:39] Indexing splices
[2018-10-13 00:40:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:40:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:40:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:40:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:41:00] Joining segment hits
[2018-10-13 00:42:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:42:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:42:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:42:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:42:25] Joining segment hits
[2018-10-13 00:43:41] Reporting output tracks
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[2018-10-13 00:45:22] A summary of the alignment counts can be found in /scratch/8792864.1.c/tophat2/align_summary.txt
[2018-10-13 00:45:22] Run complete: 00:15:27 elapsed