[2018-10-13 08:52:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:52:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:52:56] Checking for Bowtie index files (genome)..
[2018-10-13 08:52:56] Checking for reference FASTA file
[2018-10-13 08:52:56] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:53:01] Reading known junctions from GTF file
[2018-10-13 08:53:05] Preparing reads
	 left reads: min. length=100, max. length=100, 918185 kept reads (137 discarded)
	right reads: min. length=100, max. length=100, 917891 kept reads (431 discarded)
[2018-10-13 08:53:45] Building transcriptome data files /scratch/8793129.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:54:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:02:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:04:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:05:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:05:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:06:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:06:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:06:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:06:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:07:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:07:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:07:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:08:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:08:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:08:26] Searching for junctions via segment mapping
[2018-10-13 09:14:15] Retrieving sequences for splices
[2018-10-13 09:16:21] Indexing splices
[2018-10-13 09:16:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:16:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:17:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:17:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:17:19] Joining segment hits
[2018-10-13 09:19:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:19:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:20:04] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:20:13] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:20:23] Joining segment hits
[2018-10-13 09:22:49] Reporting output tracks
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[2018-10-13 09:44:14] A summary of the alignment counts can be found in /scratch/8793129.1.linga/tophat2/align_summary.txt
[2018-10-13 09:44:14] Run complete: 00:51:18 elapsed