[2018-10-13 08:33:07] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:33:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:33:07] Checking for Bowtie index files (genome)..
[2018-10-13 08:33:07] Checking for reference FASTA file
[2018-10-13 08:33:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:33:12] Reading known junctions from GTF file
[2018-10-13 08:33:15] Preparing reads
	 left reads: min. length=100, max. length=100, 1395816 kept reads (68 discarded)
	right reads: min. length=100, max. length=100, 1395261 kept reads (623 discarded)
[2018-10-13 08:34:09] Building transcriptome data files /scratch/8793120.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:34:28] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:42:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:43:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:44:40] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:44:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:45:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:45:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:45:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:45:40] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:45:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:46:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:46:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:46:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:47:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:47:14] Searching for junctions via segment mapping
[2018-10-13 08:51:43] Retrieving sequences for splices
[2018-10-13 08:53:46] Indexing splices
[2018-10-13 08:54:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:54:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:54:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:54:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:54:34] Joining segment hits
[2018-10-13 08:56:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:57:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:57:09] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:57:16] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:57:23] Joining segment hits
[2018-10-13 08:59:48] Reporting output tracks
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[2018-10-13 09:12:46] A summary of the alignment counts can be found in /scratch/8793120.1.linga/tophat2/align_summary.txt
[2018-10-13 09:12:46] Run complete: 00:39:38 elapsed