[2019-04-22 20:12:38] Beginning TopHat run (v2.1.1)
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[2019-04-22 20:12:38] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-22 20:12:39] Checking for Bowtie index files (genome)..
[2019-04-22 20:12:39] Checking for reference FASTA file
[2019-04-22 20:12:39] Generating SAM header for Bowtie2Index/genome
[2019-04-22 20:12:41] Reading known junctions from GTF file
[2019-04-22 20:12:43] Preparing reads
	 left reads: min. length=50, max. length=50, 34918041 kept reads (5653 discarded)
	right reads: min. length=50, max. length=50, 29219098 kept reads (5704596 discarded)
[2019-04-22 20:21:18] Building transcriptome data files /scratch/5525169.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:21:27] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:26:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:31:11] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:39:50] Resuming TopHat pipeline with unmapped reads
[2019-04-22 20:39:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 20:53:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 20:55:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 20:57:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:15:44] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:28:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:40:14] Searching for junctions via segment mapping
[2019-04-22 21:42:48] Retrieving sequences for splices
[2019-04-22 21:43:48] Indexing splices
Building a SMALL index
[2019-04-22 21:44:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 21:44:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 21:45:08] Joining segment hits
[2019-04-22 21:46:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 21:50:06] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 21:51:33] Joining segment hits
[2019-04-22 21:53:34] Reporting output tracks
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[2019-04-22 22:08:04] A summary of the alignment counts can be found in /scratch/5525169.1.linga/tophat2/align_summary.txt
[2019-04-22 22:08:04] Run complete: 01:55:25 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 14 files...