[2018-10-13 11:49:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:49:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:49:57] Checking for Bowtie index files (genome)..
[2018-10-13 11:49:57] Checking for reference FASTA file
[2018-10-13 11:49:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:50:01] Reading known junctions from GTF file
[2018-10-13 11:50:06] Preparing reads
	 left reads: min. length=100, max. length=100, 1167090 kept reads (135 discarded)
	right reads: min. length=100, max. length=100, 1166880 kept reads (345 discarded)
[2018-10-13 11:50:50] Building transcriptome data files /scratch/8793218.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:51:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:59:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:00:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:02:03] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:02:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:02:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:03:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:03:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:03:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:03:50] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:04:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:04:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:05:10] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:05:24] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:05:38] Searching for junctions via segment mapping
[2018-10-13 12:12:35] Retrieving sequences for splices
[2018-10-13 12:14:51] Indexing splices
[2018-10-13 12:15:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:15:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:15:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:15:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:15:58] Joining segment hits
[2018-10-13 12:18:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:18:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:18:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:19:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:19:10] Joining segment hits
[2018-10-13 12:21:54] Reporting output tracks
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[2018-10-13 12:40:53] A summary of the alignment counts can be found in /scratch/8793218.1.linga/tophat2/align_summary.txt
[2018-10-13 12:40:53] Run complete: 00:50:56 elapsed