[2017-06-16 10:19:48] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:19:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:19:48] Checking for Bowtie index files (genome)..
[2017-06-16 10:19:48] Checking for reference FASTA file
[2017-06-16 10:19:48] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:19:51] Reading known junctions from GTF file
[2017-06-16 10:19:53] Preparing reads
	 left reads: min. length=101, max. length=101, 18270067 kept reads (44 discarded)
	right reads: min. length=101, max. length=101, 18222521 kept reads (47590 discarded)
[2017-06-16 10:30:14] Building transcriptome data files /scratch/9351458.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:30:22] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:31:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:37:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:43:02] Resuming TopHat pipeline with unmapped reads
[2017-06-16 10:43:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 10:48:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 10:48:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 10:49:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 10:50:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 10:51:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 10:57:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 10:58:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 10:59:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:00:52] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:02:26] Searching for junctions via segment mapping
[2017-06-16 11:28:42] Retrieving sequences for splices
[2017-06-16 11:29:47] Indexing splices
[2017-06-16 11:30:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 11:30:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 11:31:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 11:32:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 11:33:06] Joining segment hits
[2017-06-16 11:34:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 11:35:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 11:36:34] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 11:37:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 11:38:16] Joining segment hits
[2017-06-16 11:40:13] Reporting output tracks
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[2017-06-16 11:52:29] A summary of the alignment counts can be found in /scratch/9351458.1.linga/tophat2/align_summary.txt
[2017-06-16 11:52:29] Run complete: 01:32:41 elapsed