[2019-05-08 09:23:04] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:23:04] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:23:04] Checking for Bowtie index files (genome)..
[2019-05-08 09:23:04] Checking for reference FASTA file
[2019-05-08 09:23:04] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:23:14] Reading known junctions from GTF file
[2019-05-08 09:23:18] Preparing reads
	 left reads: min. length=101, max. length=101, 33052537 kept reads (175966 discarded)
[2019-05-08 09:35:47] Building transcriptome data files /scratch/5992734.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:36:06] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:49:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:08:50] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:08:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:34:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:36:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:39:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:43:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:46:15] Searching for junctions via segment mapping
[2019-05-08 10:55:39] Retrieving sequences for splices
[2019-05-08 10:57:56] Indexing splices
[2019-05-08 10:59:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 10:59:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 11:01:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 11:02:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 11:03:01] Joining segment hits
[2019-05-08 11:06:48] Reporting output tracks
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[2019-05-08 11:31:22] A summary of the alignment counts can be found in /scratch/5992734.1.linga/tophat2/align_summary.txt
[2019-05-08 11:31:22] Run complete: 02:08:17 elapsed