[2018-10-13 00:46:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:46:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:46:03] Checking for Bowtie index files (genome)..
[2018-10-13 00:46:03] Checking for reference FASTA file
[2018-10-13 00:46:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:46:07] Reading known junctions from GTF file
[2018-10-13 00:46:12] Preparing reads
	 left reads: min. length=100, max. length=100, 190587 kept reads (93 discarded)
	right reads: min. length=100, max. length=100, 190480 kept reads (200 discarded)
[2018-10-13 00:46:21] Building transcriptome data files /scratch/8792870.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:46:41] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:55:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:55:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:55:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:55:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:56:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:56:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:56:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:56:36] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:56:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:57:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:57:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:57:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:57:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:57:50] Searching for junctions via segment mapping
[2018-10-13 01:00:19] Retrieving sequences for splices
[2018-10-13 01:02:28] Indexing splices
[2018-10-13 01:02:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:02:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:02:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:03:01] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:03:05] Joining segment hits
[2018-10-13 01:05:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:05:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:05:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:05:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:05:37] Joining segment hits
[2018-10-13 01:07:51] Reporting output tracks
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[2018-10-13 01:10:40] A summary of the alignment counts can be found in /scratch/8792870.1.linga/tophat2/align_summary.txt
[2018-10-13 01:10:40] Run complete: 00:24:37 elapsed