[2018-10-13 08:50:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:50:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:50:34] Checking for Bowtie index files (genome)..
[2018-10-13 08:50:34] Checking for reference FASTA file
[2018-10-13 08:50:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:50:38] Reading known junctions from GTF file
[2018-10-13 08:50:42] Preparing reads
	 left reads: min. length=100, max. length=100, 1963185 kept reads (121 discarded)
	right reads: min. length=100, max. length=100, 1962710 kept reads (596 discarded)
[2018-10-13 08:52:02] Building transcriptome data files /scratch/8793127.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:52:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:00:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:01:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:03:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:03:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:04:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:04:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:04:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:04:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:05:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:05:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:06:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:06:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:06:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:06:54] Searching for junctions via segment mapping
[2018-10-13 09:11:40] Retrieving sequences for splices
[2018-10-13 09:13:45] Indexing splices
[2018-10-13 09:14:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:14:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:14:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:14:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:14:40] Joining segment hits
[2018-10-13 09:17:08] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:17:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:17:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:17:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:17:38] Joining segment hits
[2018-10-13 09:20:01] Reporting output tracks
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[2018-10-13 09:35:09] A summary of the alignment counts can be found in /scratch/8793127.1.linga/tophat2/align_summary.txt
[2018-10-13 09:35:09] Run complete: 00:44:35 elapsed