[2017-06-14 21:34:24] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:24] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:25] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:25] Checking for reference FASTA file
[2017-06-14 21:34:25] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:29] Reading known junctions from GTF file
[2017-06-14 21:34:32] Preparing reads
	 left reads: min. length=101, max. length=101, 16537304 kept reads (33 discarded)
	right reads: min. length=101, max. length=101, 16494352 kept reads (42985 discarded)
[2017-06-14 21:51:21] Building transcriptome data files /scratch/9328378.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:51:36] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:53:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:04:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:16:00] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:16:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:26:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:28:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:30:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:32:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:34:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:48:11] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:50:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:53:37] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:59:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:03:50] Searching for junctions via segment mapping
[2017-06-14 23:14:12] Retrieving sequences for splices
[2017-06-14 23:16:33] Indexing splices
Building a SMALL index
[2017-06-14 23:17:23] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:18:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:18:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:19:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:20:36] Joining segment hits
[2017-06-14 23:23:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:24:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:25:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:26:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:27:56] Joining segment hits
[2017-06-14 23:31:44] Reporting output tracks
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[2017-06-14 23:52:50] A summary of the alignment counts can be found in /scratch/9328378.1.linga/tophat2/align_summary.txt
[2017-06-14 23:52:50] Run complete: 02:18:25 elapsed
[samopen] SAM header is present: 23 sequences.
[bam_sort_core] merging from 11 files...