[2019-04-22 20:11:49] Beginning TopHat run (v2.1.1)
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[2019-04-22 20:11:49] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-22 20:11:49] Checking for Bowtie index files (genome)..
[2019-04-22 20:11:49] Checking for reference FASTA file
[2019-04-22 20:11:49] Generating SAM header for Bowtie2Index/genome
[2019-04-22 20:11:54] Reading known junctions from GTF file
[2019-04-22 20:11:58] Preparing reads
	 left reads: min. length=50, max. length=50, 20814415 kept reads (3472 discarded)
	right reads: min. length=50, max. length=50, 17979082 kept reads (2838805 discarded)
[2019-04-22 20:20:06] Building transcriptome data files /scratch/5525172.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:20:23] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:28:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:38:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:53:21] Resuming TopHat pipeline with unmapped reads
[2019-04-22 20:53:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:11:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:13:45] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:16:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:38:56] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:57:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 22:17:22] Searching for junctions via segment mapping
[2019-04-22 22:23:01] Retrieving sequences for splices
[2019-04-22 22:25:16] Indexing splices
Building a SMALL index
[2019-04-22 22:25:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 22:26:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 22:26:39] Joining segment hits
[2019-04-22 22:29:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 22:32:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 22:35:13] Joining segment hits
[2019-04-22 22:39:34] Reporting output tracks
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[2019-04-22 23:15:01] A summary of the alignment counts can be found in /scratch/5525172.1.linga/tophat2/align_summary.txt
[2019-04-22 23:15:01] Run complete: 03:03:12 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 12 files...