[2018-10-13 18:32:21] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:32:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:32:21] Checking for Bowtie index files (genome)..
[2018-10-13 18:32:21] Checking for reference FASTA file
[2018-10-13 18:32:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:32:25] Reading known junctions from GTF file
[2018-10-13 18:32:29] Preparing reads
	 left reads: min. length=100, max. length=100, 405183 kept reads (158 discarded)
	right reads: min. length=100, max. length=100, 404904 kept reads (437 discarded)
[2018-10-13 18:32:48] Building transcriptome data files /scratch/8793440.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:33:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:41:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:41:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:42:18] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:42:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:42:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:43:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:43:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:43:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:43:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:44:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:44:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:44:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:44:59] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:45:09] Searching for junctions via segment mapping
[2018-10-13 18:47:59] Retrieving sequences for splices
[2018-10-13 18:50:11] Indexing splices
[2018-10-13 18:50:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:50:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:50:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:50:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:50:50] Joining segment hits
[2018-10-13 18:53:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:53:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:53:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:53:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:53:34] Joining segment hits
[2018-10-13 18:56:02] Reporting output tracks
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[2018-10-13 18:59:33] A summary of the alignment counts can be found in /scratch/8793440.1.linga/tophat2/align_summary.txt
[2018-10-13 18:59:33] Run complete: 00:27:11 elapsed