[2019-04-22 20:12:47] Beginning TopHat run (v2.1.1)
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[2019-04-22 20:12:47] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-22 20:12:47] Checking for Bowtie index files (genome)..
[2019-04-22 20:12:47] Checking for reference FASTA file
[2019-04-22 20:12:47] Generating SAM header for Bowtie2Index/genome
[2019-04-22 20:12:51] Reading known junctions from GTF file
[2019-04-22 20:12:55] Preparing reads
	 left reads: min. length=50, max. length=50, 30649657 kept reads (3818 discarded)
	right reads: min. length=50, max. length=50, 27120566 kept reads (3532909 discarded)
[2019-04-22 20:26:05] Building transcriptome data files /scratch/5525166.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:26:25] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:34:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:48:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 21:03:01] Resuming TopHat pipeline with unmapped reads
[2019-04-22 21:03:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:20:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:24:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:27:57] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:56:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 22:29:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 23:01:35] Searching for junctions via segment mapping
[2019-04-22 23:08:23] Retrieving sequences for splices
[2019-04-22 23:10:48] Indexing splices
Building a SMALL index
[2019-04-22 23:11:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:12:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 23:13:29] Joining segment hits
[2019-04-22 23:16:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:31:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 23:36:54] Joining segment hits
[2019-04-22 23:42:31] Reporting output tracks
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[2019-04-23 00:19:40] A summary of the alignment counts can be found in /scratch/5525166.1.linga/tophat2/align_summary.txt
[2019-04-23 00:19:40] Run complete: 04:06:52 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 16 files...