[2019-06-26 14:05:20] Beginning TopHat run (v2.1.1)
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[2019-06-26 14:05:20] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 14:05:21] Checking for Bowtie index files (genome)..
[2019-06-26 14:05:21] Checking for reference FASTA file
[2019-06-26 14:05:21] Generating SAM header for Bowtie2Index/genome
[2019-06-26 14:05:26] Reading known junctions from GTF file
[2019-06-26 14:05:30] Preparing reads
	 left reads: min. length=51, max. length=51, 32980218 kept reads (51641 discarded)
	right reads: min. length=51, max. length=51, 33015791 kept reads (16068 discarded)
[2019-06-26 14:24:31] Building transcriptome data files /scratch/7076166.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 14:24:51] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 14:31:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 14:46:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 14:59:21] Resuming TopHat pipeline with unmapped reads
[2019-06-26 14:59:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 15:10:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 15:11:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 15:12:58] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 15:24:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-06-26 15:25:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-06-26 15:26:37] Searching for junctions via segment mapping
[2019-06-26 15:31:52] Retrieving sequences for splices
[2019-06-26 15:34:02] Indexing splices
[2019-06-26 15:34:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 15:34:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 15:34:35] Joining segment hits
[2019-06-26 15:37:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-06-26 15:37:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-06-26 15:37:36] Joining segment hits
[2019-06-26 15:40:11] Reporting output tracks
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[2019-06-26 17:05:14] A summary of the alignment counts can be found in /scratch/7076166.1.linga/tophat2/align_summary.txt
[2019-06-26 17:05:14] Run complete: 02:59:53 elapsed