[2019-05-08 09:08:47] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:08:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:08:48] Checking for Bowtie index files (genome)..
[2019-05-08 09:08:48] Checking for reference FASTA file
[2019-05-08 09:08:48] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:08:52] Reading known junctions from GTF file
[2019-05-08 09:08:56] Preparing reads
	 left reads: min. length=101, max. length=101, 41204798 kept reads (319828 discarded)
[2019-05-08 09:27:19] Building transcriptome data files /scratch/5992729.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:28:50] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:37:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:03:38] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:03:38] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:19:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:21:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:23:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:25:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:27:17] Searching for junctions via segment mapping
[2019-05-08 10:33:52] Retrieving sequences for splices
[2019-05-08 10:35:45] Indexing splices
[2019-05-08 10:36:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 10:37:05] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 10:37:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 10:38:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 10:38:51] Joining segment hits
[2019-05-08 10:41:55] Reporting output tracks
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[2019-05-08 11:08:46] A summary of the alignment counts can be found in /scratch/5992729.1.linga/tophat2/align_summary.txt
[2019-05-08 11:08:46] Run complete: 01:59:58 elapsed