[2018-10-13 16:50:50] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:50:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:50:50] Checking for Bowtie index files (genome)..
[2018-10-13 16:50:50] Checking for reference FASTA file
[2018-10-13 16:50:50] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:50:55] Reading known junctions from GTF file
[2018-10-13 16:50:59] Preparing reads
	 left reads: min. length=100, max. length=100, 239942 kept reads (105 discarded)
	right reads: min. length=100, max. length=100, 239690 kept reads (357 discarded)
[2018-10-13 16:51:08] Building transcriptome data files /scratch/8793374.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:51:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:59:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:00:00] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:00:22] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:00:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:00:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:00:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:01:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:01:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:01:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:01:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:01:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:01:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:02:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:02:16] Searching for junctions via segment mapping
[2018-10-13 17:04:53] Retrieving sequences for splices
[2018-10-13 17:07:02] Indexing splices
[2018-10-13 17:07:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:07:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:07:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:07:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:07:41] Joining segment hits
[2018-10-13 17:10:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:10:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:10:20] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:10:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:10:28] Joining segment hits
[2018-10-13 17:12:45] Reporting output tracks
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[2018-10-13 17:15:54] A summary of the alignment counts can be found in /scratch/8793374.1.linga/tophat2/align_summary.txt
[2018-10-13 17:15:54] Run complete: 00:25:03 elapsed