[2019-05-08 09:21:48] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:21:48] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:21:48] Checking for Bowtie index files (genome)..
[2019-05-08 09:21:48] Checking for reference FASTA file
[2019-05-08 09:21:48] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:21:52] Reading known junctions from GTF file
[2019-05-08 09:21:57] Preparing reads
	 left reads: min. length=101, max. length=101, 34634964 kept reads (204213 discarded)
[2019-05-08 09:35:41] Building transcriptome data files /scratch/5992733.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:36:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:44:31] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:25:00] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:25:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:39:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:41:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:43:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:45:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:47:58] Searching for junctions via segment mapping
[2019-05-08 11:11:51] Retrieving sequences for splices
[2019-05-08 11:13:59] Indexing splices
[2019-05-08 11:15:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 11:17:09] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 11:18:31] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 11:19:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 11:20:59] Joining segment hits
[2019-05-08 11:25:01] Reporting output tracks
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[2019-05-08 11:47:43] A summary of the alignment counts can be found in /scratch/5992733.1.linga/tophat2/align_summary.txt
[2019-05-08 11:47:43] Run complete: 02:25:55 elapsed