[2018-10-13 09:32:11] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:32:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:32:11] Checking for Bowtie index files (genome)..
[2018-10-13 09:32:11] Checking for reference FASTA file
[2018-10-13 09:32:11] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:32:15] Reading known junctions from GTF file
[2018-10-13 09:32:20] Preparing reads
	 left reads: min. length=100, max. length=100, 119793 kept reads (107 discarded)
	right reads: min. length=100, max. length=100, 119685 kept reads (215 discarded)
[2018-10-13 09:32:25] Building transcriptome data files /scratch/8793148.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:32:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:40:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:40:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:40:30] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:40:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:40:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:40:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:41:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:41:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:41:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:41:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:41:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:41:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:42:04] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:42:12] Searching for junctions via segment mapping
[2018-10-13 09:44:22] Retrieving sequences for splices
[2018-10-13 09:46:29] Indexing splices
[2018-10-13 09:46:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:46:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:46:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:46:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:47:03] Joining segment hits
[2018-10-13 09:49:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:49:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:49:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:49:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:49:31] Joining segment hits
[2018-10-13 09:51:43] Reporting output tracks
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[2018-10-13 09:54:05] A summary of the alignment counts can be found in /scratch/8793148.1.linga/tophat2/align_summary.txt
[2018-10-13 09:54:05] Run complete: 00:21:54 elapsed