[2018-10-13 15:53:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 15:53:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:53:31] Checking for Bowtie index files (genome)..
[2018-10-13 15:53:31] Checking for reference FASTA file
[2018-10-13 15:53:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:53:35] Reading known junctions from GTF file
[2018-10-13 15:53:40] Preparing reads
	 left reads: min. length=100, max. length=100, 254150 kept reads (158 discarded)
	right reads: min. length=100, max. length=100, 253930 kept reads (378 discarded)
[2018-10-13 15:53:51] Building transcriptome data files /scratch/8793333.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:54:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:02:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:02:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:03:22] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:03:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:03:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:03:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:04:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:04:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:04:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:04:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:04:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:04:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:05:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:05:16] Searching for junctions via segment mapping
[2018-10-13 16:09:25] Retrieving sequences for splices
[2018-10-13 16:11:42] Indexing splices
[2018-10-13 16:12:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:12:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:12:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:12:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:12:21] Joining segment hits
[2018-10-13 16:14:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:14:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:14:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:14:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:15:01] Joining segment hits
[2018-10-13 16:17:27] Reporting output tracks
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[2018-10-13 16:22:43] A summary of the alignment counts can be found in /scratch/8793333.1.linga/tophat2/align_summary.txt
[2018-10-13 16:22:43] Run complete: 00:29:11 elapsed