[2018-10-13 14:26:18] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:26:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:26:18] Checking for Bowtie index files (genome)..
[2018-10-13 14:26:18] Checking for reference FASTA file
[2018-10-13 14:26:18] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:26:22] Reading known junctions from GTF file
[2018-10-13 14:26:26] Preparing reads
	 left reads: min. length=100, max. length=100, 1643165 kept reads (127 discarded)
	right reads: min. length=100, max. length=100, 1642727 kept reads (565 discarded)
[2018-10-13 14:27:33] Building transcriptome data files /scratch/8793289.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:27:52] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:35:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:37:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:38:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:38:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:39:31] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:39:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:39:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:40:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:40:23] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:41:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:41:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:41:42] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:41:56] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:42:10] Searching for junctions via segment mapping
[2018-10-13 14:47:24] Retrieving sequences for splices
[2018-10-13 14:49:36] Indexing splices
Building a SMALL index
[2018-10-13 14:50:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:50:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:50:18] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:50:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:50:34] Joining segment hits
[2018-10-13 14:53:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:53:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:53:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:53:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:53:38] Joining segment hits
[2018-10-13 14:56:19] Reporting output tracks
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[2018-10-13 15:13:46] A summary of the alignment counts can be found in /scratch/8793289.1.linga/tophat2/align_summary.txt
[2018-10-13 15:13:46] Run complete: 00:47:27 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...