[2019-05-08 09:21:01] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-05-08 09:21:01] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:21:02] Checking for Bowtie index files (genome)..
[2019-05-08 09:21:02] Checking for reference FASTA file
[2019-05-08 09:21:02] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:21:08] Reading known junctions from GTF file
[2019-05-08 09:21:13] Preparing reads
	 left reads: min. length=101, max. length=101, 34874295 kept reads (214569 discarded)
[2019-05-08 09:35:22] Building transcriptome data files /scratch/5992732.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:35:44] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:44:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:15:32] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:15:32] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:36:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:39:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:42:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:46:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:50:01] Searching for junctions via segment mapping
[2019-05-08 11:10:20] Retrieving sequences for splices
[2019-05-08 11:12:30] Indexing splices
[2019-05-08 11:13:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 11:15:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 11:16:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 11:17:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 11:19:17] Joining segment hits
[2019-05-08 11:22:39] Reporting output tracks
-----------------------------------------------
[2019-05-08 11:42:21] A summary of the alignment counts can be found in /scratch/5992732.1.linga/tophat2/align_summary.txt
[2019-05-08 11:42:21] Run complete: 02:21:19 elapsed