[2018-10-13 10:57:37] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:57:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:57:37] Checking for Bowtie index files (genome)..
[2018-10-13 10:57:37] Checking for reference FASTA file
[2018-10-13 10:57:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:57:42] Reading known junctions from GTF file
[2018-10-13 10:57:46] Preparing reads
	 left reads: min. length=100, max. length=100, 620872 kept reads (59 discarded)
	right reads: min. length=100, max. length=100, 620565 kept reads (366 discarded)
[2018-10-13 10:58:11] Building transcriptome data files /scratch/8793189.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:58:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:06:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:06:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:07:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:07:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:07:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:07:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:07:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:08:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:08:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:08:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:08:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:09:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:09:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:09:19] Searching for junctions via segment mapping
[2018-10-13 11:12:35] Retrieving sequences for splices
[2018-10-13 11:14:52] Indexing splices
[2018-10-13 11:15:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:15:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:15:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:15:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:15:31] Joining segment hits
[2018-10-13 11:17:51] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:17:56] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:18:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:18:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:18:10] Joining segment hits
[2018-10-13 11:20:31] Reporting output tracks
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[2018-10-13 11:24:48] A summary of the alignment counts can be found in /scratch/8793189.1.linga/tophat2/align_summary.txt
[2018-10-13 11:24:48] Run complete: 00:27:11 elapsed