[2018-10-13 06:04:52] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:04:52] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:04:52] Checking for Bowtie index files (genome)..
[2018-10-13 06:04:52] Checking for reference FASTA file
[2018-10-13 06:04:52] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:04:57] Reading known junctions from GTF file
[2018-10-13 06:05:02] Preparing reads
	 left reads: min. length=100, max. length=100, 173301 kept reads (44 discarded)
	right reads: min. length=100, max. length=100, 173221 kept reads (124 discarded)
[2018-10-13 06:05:09] Building transcriptome data files /scratch/8793043.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:05:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:13:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:13:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:13:58] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:13:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:14:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:14:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:14:24] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:14:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:14:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:14:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:14:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:15:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:15:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:15:21] Searching for junctions via segment mapping
[2018-10-13 06:17:55] Retrieving sequences for splices
[2018-10-13 06:20:06] Indexing splices
[2018-10-13 06:20:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:20:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:20:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:20:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:20:44] Joining segment hits
[2018-10-13 06:22:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:23:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:23:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:23:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:23:15] Joining segment hits
[2018-10-13 06:25:33] Reporting output tracks
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[2018-10-13 06:28:41] A summary of the alignment counts can be found in /scratch/8793043.1.linga/tophat2/align_summary.txt
[2018-10-13 06:28:41] Run complete: 00:23:48 elapsed