[2018-10-13 18:34:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:34:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:34:32] Checking for Bowtie index files (genome)..
[2018-10-13 18:34:32] Checking for reference FASTA file
[2018-10-13 18:34:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:34:36] Reading known junctions from GTF file
[2018-10-13 18:34:40] Preparing reads
	 left reads: min. length=100, max. length=100, 237994 kept reads (246 discarded)
	right reads: min. length=100, max. length=100, 237984 kept reads (256 discarded)
[2018-10-13 18:34:51] Building transcriptome data files /scratch/8793443.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:35:10] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:43:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:43:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:43:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:43:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:44:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:44:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:44:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:44:52] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:45:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:45:32] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:45:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:45:51] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:46:00] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:46:09] Searching for junctions via segment mapping
[2018-10-13 18:48:36] Retrieving sequences for splices
[2018-10-13 18:50:38] Indexing splices
[2018-10-13 18:50:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:51:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:51:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:51:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:51:13] Joining segment hits
[2018-10-13 18:53:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:53:28] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:53:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:53:37] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:53:42] Joining segment hits
[2018-10-13 18:55:47] Reporting output tracks
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[2018-10-13 18:58:38] A summary of the alignment counts can be found in /scratch/8793443.1.linga/tophat2/align_summary.txt
[2018-10-13 18:58:38] Run complete: 00:24:05 elapsed