[2018-10-13 08:26:37] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:26:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:26:37] Checking for Bowtie index files (genome)..
[2018-10-13 08:26:37] Checking for reference FASTA file
[2018-10-13 08:26:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:26:41] Reading known junctions from GTF file
[2018-10-13 08:26:46] Preparing reads
	 left reads: min. length=100, max. length=100, 1560448 kept reads (129 discarded)
	right reads: min. length=100, max. length=100, 1559900 kept reads (677 discarded)
[2018-10-13 08:27:56] Building transcriptome data files /scratch/8793113.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:28:16] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:35:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:36:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:37:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:37:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:38:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:38:48] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:39:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:39:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:39:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:40:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:40:17] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:40:32] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:40:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:40:57] Searching for junctions via segment mapping
[2018-10-13 08:45:38] Retrieving sequences for splices
[2018-10-13 08:47:38] Indexing splices
Building a SMALL index
[2018-10-13 08:47:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:48:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:48:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:48:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:48:26] Joining segment hits
[2018-10-13 08:50:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:50:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:51:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:51:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:51:16] Joining segment hits
[2018-10-13 08:53:39] Reporting output tracks
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[2018-10-13 09:06:45] A summary of the alignment counts can be found in /scratch/8793113.1.linga/tophat2/align_summary.txt
[2018-10-13 09:06:45] Run complete: 00:40:07 elapsed
[samopen] SAM header is present: 114 sequences.
[bam_sort_core] merging from 2 files...