[2018-10-13 16:28:40] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:28:40] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:28:40] Checking for Bowtie index files (genome)..
[2018-10-13 16:28:40] Checking for reference FASTA file
[2018-10-13 16:28:40] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:28:46] Reading known junctions from GTF file
[2018-10-13 16:28:50] Preparing reads
	 left reads: min. length=100, max. length=100, 349447 kept reads (467 discarded)
	right reads: min. length=100, max. length=100, 349184 kept reads (730 discarded)
[2018-10-13 16:29:06] Building transcriptome data files /scratch/8793357.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:29:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:37:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:38:21] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:39:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:39:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:39:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:39:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:40:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:40:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:40:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:41:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:41:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:41:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:41:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:41:52] Searching for junctions via segment mapping
[2018-10-13 16:45:21] Retrieving sequences for splices
[2018-10-13 16:47:34] Indexing splices
[2018-10-13 16:47:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:48:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:48:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:48:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:48:20] Joining segment hits
[2018-10-13 16:51:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:51:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:51:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:51:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:51:24] Joining segment hits
[2018-10-13 16:53:48] Reporting output tracks
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[2018-10-13 16:59:00] A summary of the alignment counts can be found in /scratch/8793357.1.linga/tophat2/align_summary.txt
[2018-10-13 16:59:00] Run complete: 00:30:19 elapsed