[2019-04-22 20:13:36] Beginning TopHat run (v2.1.1)
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[2019-04-22 20:13:36] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-22 20:13:36] Checking for Bowtie index files (genome)..
[2019-04-22 20:13:36] Checking for reference FASTA file
[2019-04-22 20:13:36] Generating SAM header for Bowtie2Index/genome
[2019-04-22 20:13:40] Reading known junctions from GTF file
[2019-04-22 20:13:44] Preparing reads
	 left reads: min. length=50, max. length=50, 34004813 kept reads (6490 discarded)
	right reads: min. length=50, max. length=50, 28294673 kept reads (5716630 discarded)
[2019-04-22 20:27:08] Building transcriptome data files /scratch/5525173.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:27:24] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:34:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:47:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:59:54] Resuming TopHat pipeline with unmapped reads
[2019-04-22 20:59:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:25:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:31:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:38:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 22:12:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 22:52:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 23:25:27] Searching for junctions via segment mapping
[2019-04-22 23:31:54] Retrieving sequences for splices
[2019-04-22 23:34:16] Indexing splices
Building a SMALL index
[2019-04-22 23:34:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:36:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 23:37:46] Joining segment hits
[2019-04-22 23:40:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:56:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-23 00:01:32] Joining segment hits
[2019-04-23 00:06:36] Reporting output tracks
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[2019-04-23 00:39:17] A summary of the alignment counts can be found in /scratch/5525173.1.linga/tophat2/align_summary.txt
[2019-04-23 00:39:17] Run complete: 04:25:41 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 14 files...