[2019-05-08 09:05:30] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:05:30] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:05:32] Checking for Bowtie index files (genome)..
[2019-05-08 09:05:32] Checking for reference FASTA file
[2019-05-08 09:05:32] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:05:39] Reading known junctions from GTF file
[2019-05-08 09:05:43] Preparing reads
	 left reads: min. length=101, max. length=101, 31937183 kept reads (193611 discarded)
[2019-05-08 09:17:39] Building transcriptome data files /scratch/5992728.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:17:57] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:26:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:07:20] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:07:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:21:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:22:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:24:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:26:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:27:54] Searching for junctions via segment mapping
[2019-05-08 10:55:14] Retrieving sequences for splices
[2019-05-08 10:57:26] Indexing splices
[2019-05-08 10:59:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 11:00:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 11:01:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 11:03:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 11:04:26] Joining segment hits
[2019-05-08 11:07:57] Reporting output tracks
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[2019-05-08 11:35:38] A summary of the alignment counts can be found in /scratch/5992728.1.linga/tophat2/align_summary.txt
[2019-05-08 11:35:38] Run complete: 02:30:09 elapsed