[2018-10-13 09:13:27] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:13:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:13:27] Checking for Bowtie index files (genome)..
[2018-10-13 09:13:27] Checking for reference FASTA file
[2018-10-13 09:13:27] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:13:32] Reading known junctions from GTF file
[2018-10-13 09:13:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1398979 kept reads (75 discarded)
	right reads: min. length=100, max. length=100, 1398558 kept reads (496 discarded)
[2018-10-13 09:14:38] Building transcriptome data files /scratch/8793141.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:14:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:23:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:24:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:25:07] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:25:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:25:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:25:59] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:26:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:26:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:26:38] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:27:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:27:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:27:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:27:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:28:09] Searching for junctions via segment mapping
[2018-10-13 09:32:04] Retrieving sequences for splices
[2018-10-13 09:34:13] Indexing splices
[2018-10-13 09:34:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:34:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:34:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:34:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:34:55] Joining segment hits
[2018-10-13 09:37:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:37:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:37:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:37:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:37:42] Joining segment hits
[2018-10-13 09:40:07] Reporting output tracks
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[2018-10-13 09:48:32] A summary of the alignment counts can be found in /scratch/8793141.1.linga/tophat2/align_summary.txt
[2018-10-13 09:48:32] Run complete: 00:35:04 elapsed