[2019-04-22 20:13:16] Beginning TopHat run (v2.1.1)
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[2019-04-22 20:13:16] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-22 20:13:16] Checking for Bowtie index files (genome)..
[2019-04-22 20:13:16] Checking for reference FASTA file
[2019-04-22 20:13:16] Generating SAM header for Bowtie2Index/genome
[2019-04-22 20:13:20] Reading known junctions from GTF file
[2019-04-22 20:13:24] Preparing reads
	 left reads: min. length=50, max. length=50, 41187532 kept reads (3713 discarded)
	right reads: min. length=50, max. length=50, 35292020 kept reads (5899225 discarded)
[2019-04-22 20:30:53] Building transcriptome data files /scratch/5525164.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:31:18] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:40:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:59:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 21:18:30] Resuming TopHat pipeline with unmapped reads
[2019-04-22 21:18:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:39:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:43:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:48:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 22:31:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 23:12:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 23:46:20] Searching for junctions via segment mapping
[2019-04-22 23:53:01] Retrieving sequences for splices
[2019-04-22 23:55:06] Indexing splices
Building a SMALL index
[2019-04-22 23:55:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:56:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 23:57:27] Joining segment hits
[2019-04-23 00:00:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-23 00:09:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-23 00:15:44] Joining segment hits
[2019-04-23 00:21:05] Reporting output tracks
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[2019-04-23 00:56:31] A summary of the alignment counts can be found in /scratch/5525164.1.linga/tophat2/align_summary.txt
[2019-04-23 00:56:31] Run complete: 04:43:14 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 22 files...