[2018-10-13 01:31:19] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:31:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:31:23] Checking for Bowtie index files (genome)..
[2018-10-13 01:31:23] Checking for reference FASTA file
[2018-10-13 01:31:23] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:31:30] Reading known junctions from GTF file
[2018-10-13 01:31:36] Preparing reads
	 left reads: min. length=100, max. length=100, 343020 kept reads (246 discarded)
	right reads: min. length=100, max. length=100, 342696 kept reads (570 discarded)
[2018-10-13 01:31:51] Building transcriptome data files /scratch/8792888.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:32:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:41:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:42:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:42:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:42:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:43:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:43:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:43:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:44:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:44:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:45:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:45:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:45:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:45:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:45:51] Searching for junctions via segment mapping
[2018-10-13 01:48:37] Retrieving sequences for splices
[2018-10-13 01:50:53] Indexing splices
[2018-10-13 01:51:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:51:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:51:25] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:51:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:51:35] Joining segment hits
[2018-10-13 01:54:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:54:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:54:39] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:54:44] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:54:48] Joining segment hits
[2018-10-13 01:57:09] Reporting output tracks
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[2018-10-13 02:00:43] A summary of the alignment counts can be found in /scratch/8792888.1.linga/tophat2/align_summary.txt
[2018-10-13 02:00:43] Run complete: 00:29:24 elapsed