[2019-05-08 09:11:07] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:11:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:11:08] Checking for Bowtie index files (genome)..
[2019-05-08 09:11:08] Checking for reference FASTA file
[2019-05-08 09:11:08] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:12:47] Reading known junctions from GTF file
[2019-05-08 09:12:51] Preparing reads
	 left reads: min. length=101, max. length=101, 35886602 kept reads (226451 discarded)
[2019-05-08 09:36:14] Building transcriptome data files /scratch/5992730.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:36:36] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:46:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:22:05] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:22:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:38:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:40:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:42:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:44:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:46:20] Searching for junctions via segment mapping
[2019-05-08 11:08:16] Retrieving sequences for splices
[2019-05-08 11:10:33] Indexing splices
[2019-05-08 11:12:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 11:13:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 11:14:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 11:16:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 11:17:13] Joining segment hits
[2019-05-08 11:20:41] Reporting output tracks
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[2019-05-08 11:40:38] A summary of the alignment counts can be found in /scratch/5992730.1.linga/tophat2/align_summary.txt
[2019-05-08 11:40:38] Run complete: 02:29:30 elapsed