[2018-10-13 10:33:48] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:33:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:33:48] Checking for Bowtie index files (genome)..
[2018-10-13 10:33:48] Checking for reference FASTA file
[2018-10-13 10:33:48] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:33:52] Reading known junctions from GTF file
[2018-10-13 10:33:57] Preparing reads
	 left reads: min. length=100, max. length=100, 962312 kept reads (132 discarded)
	right reads: min. length=100, max. length=100, 962006 kept reads (438 discarded)
[2018-10-13 10:34:38] Building transcriptome data files /scratch/8793180.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:34:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:44:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:44:58] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:46:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:46:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:46:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:46:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:47:09] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:47:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:47:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:48:20] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:48:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:48:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:48:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:49:08] Searching for junctions via segment mapping
[2018-10-13 10:54:01] Retrieving sequences for splices
[2018-10-13 10:56:06] Indexing splices
[2018-10-13 10:56:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:56:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:56:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:56:46] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:56:52] Joining segment hits
[2018-10-13 10:59:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:59:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:59:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:59:39] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:59:46] Joining segment hits
[2018-10-13 11:02:15] Reporting output tracks
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[2018-10-13 11:14:02] A summary of the alignment counts can be found in /scratch/8793180.1.linga/tophat2/align_summary.txt
[2018-10-13 11:14:02] Run complete: 00:40:13 elapsed