[2019-05-08 08:15:42] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:15:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:15:43] Checking for Bowtie index files (genome)..
[2019-05-08 08:15:43] Checking for reference FASTA file
[2019-05-08 08:15:43] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:15:47] Reading known junctions from GTF file
[2019-05-08 08:15:52] Preparing reads
	 left reads: min. length=101, max. length=101, 33151248 kept reads (451873 discarded)
[2019-05-08 08:28:34] Building transcriptome data files /scratch/5992719.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:29:27] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:37:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 08:56:17] Resuming TopHat pipeline with unmapped reads
[2019-05-08 08:56:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 09:09:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 09:11:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 09:12:30] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 09:13:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 09:15:22] Searching for junctions via segment mapping
[2019-05-08 09:19:48] Retrieving sequences for splices
[2019-05-08 09:21:48] Indexing splices
[2019-05-08 09:22:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:22:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:23:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:23:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:24:02] Joining segment hits
[2019-05-08 09:27:11] Reporting output tracks
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[2019-05-08 09:52:28] A summary of the alignment counts can be found in /scratch/5992719.1.linga/tophat2/align_summary.txt
[2019-05-08 09:52:28] Run complete: 01:36:45 elapsed