[2018-10-13 08:40:20] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:40:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:40:20] Checking for Bowtie index files (genome)..
[2018-10-13 08:40:20] Checking for reference FASTA file
[2018-10-13 08:40:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:40:25] Reading known junctions from GTF file
[2018-10-13 08:40:29] Preparing reads
	 left reads: min. length=100, max. length=100, 355208 kept reads (228 discarded)
	right reads: min. length=100, max. length=100, 354834 kept reads (602 discarded)
[2018-10-13 08:40:45] Building transcriptome data files /scratch/8793122.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:41:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:49:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:50:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:50:54] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:50:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:51:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:51:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:51:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:52:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:52:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:52:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:53:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:53:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:53:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:53:46] Searching for junctions via segment mapping
[2018-10-13 08:56:25] Retrieving sequences for splices
[2018-10-13 08:58:33] Indexing splices
[2018-10-13 08:58:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:58:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:59:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:59:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:59:10] Joining segment hits
[2018-10-13 09:01:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:01:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:01:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:01:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:01:59] Joining segment hits
[2018-10-13 09:04:38] Reporting output tracks
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[2018-10-13 09:08:07] A summary of the alignment counts can be found in /scratch/8793122.1.linga/tophat2/align_summary.txt
[2018-10-13 09:08:07] Run complete: 00:27:46 elapsed