[2017-06-14 21:34:18] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:18] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:18] Checking for reference FASTA file
[2017-06-14 21:34:18] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:24] Reading known junctions from GTF file
[2017-06-14 21:34:26] Preparing reads
	 left reads: min. length=101, max. length=101, 19120038 kept reads (81 discarded)
	right reads: min. length=101, max. length=101, 19068990 kept reads (51129 discarded)
[2017-06-14 21:53:38] Building transcriptome data files /scratch/9328376.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:53:54] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:55:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:08:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:21:11] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:21:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:32:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:34:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:37:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:39:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:41:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:56:34] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:59:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 23:02:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:06:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:10:51] Searching for junctions via segment mapping
[2017-06-14 23:20:00] Retrieving sequences for splices
[2017-06-14 23:22:31] Indexing splices
Building a SMALL index
[2017-06-14 23:23:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:24:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:25:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:25:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:26:39] Joining segment hits
[2017-06-14 23:30:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:31:17] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:32:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:33:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:34:42] Joining segment hits
[2017-06-14 23:38:49] Reporting output tracks
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[2017-06-15 00:03:39] A summary of the alignment counts can be found in /scratch/9328376.1.linga/tophat2/align_summary.txt
[2017-06-15 00:03:39] Run complete: 02:29:21 elapsed
[samopen] SAM header is present: 23 sequences.
[bam_sort_core] merging from 13 files...