[2018-10-13 06:04:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:04:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:04:53] Checking for Bowtie index files (genome)..
[2018-10-13 06:04:53] Checking for reference FASTA file
[2018-10-13 06:04:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:04:57] Reading known junctions from GTF file
[2018-10-13 06:05:02] Preparing reads
	 left reads: min. length=100, max. length=100, 641020 kept reads (78 discarded)
	right reads: min. length=100, max. length=100, 640761 kept reads (337 discarded)
[2018-10-13 06:05:27] Building transcriptome data files /scratch/8793042.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:05:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:14:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:14:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:15:20] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:15:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:15:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:15:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:16:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:16:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:16:26] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:16:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:17:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:17:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:17:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:17:32] Searching for junctions via segment mapping
[2018-10-13 06:20:48] Retrieving sequences for splices
[2018-10-13 06:23:01] Indexing splices
[2018-10-13 06:23:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:23:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:23:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:23:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:23:42] Joining segment hits
[2018-10-13 06:26:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:26:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:26:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:26:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:26:30] Joining segment hits
[2018-10-13 06:28:55] Reporting output tracks
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[2018-10-13 06:34:10] A summary of the alignment counts can be found in /scratch/8793042.1.linga/tophat2/align_summary.txt
[2018-10-13 06:34:10] Run complete: 00:29:17 elapsed