[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, 26283067 kept reads (3339 discarded)
	right reads: min. length=50, max. length=50, 22025330 kept reads (4261076 discarded)
[2019-04-22 20:22:39] Building transcriptome data files /scratch/5525170.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-22 20:22:56] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-22 20:31:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:44:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-22 20:57:20] Resuming TopHat pipeline with unmapped reads
[2019-04-22 20:57:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:19:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 21:24:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 21:31:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-22 21:58:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-22 22:31:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-22 22:56:30] Searching for junctions via segment mapping
[2019-04-22 23:02:35] Retrieving sequences for splices
[2019-04-22 23:04:49] Indexing splices
Building a SMALL index
[2019-04-22 23:05:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:06:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 23:07:41] Joining segment hits
[2019-04-22 23:10:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-22 23:14:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-22 23:16:13] Joining segment hits
[2019-04-22 23:20:10] Reporting output tracks
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[2019-04-22 23:43:49] A summary of the alignment counts can be found in /scratch/5525170.1.linga/tophat2/align_summary.txt
[2019-04-22 23:43:49] Run complete: 03:31:59 elapsed
[samopen] SAM header is present: 22 sequences.
[bam_sort_core] merging from 11 files...