[2019-05-08 09:04:20] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:04:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:04:21] Checking for Bowtie index files (genome)..
[2019-05-08 09:04:21] Checking for reference FASTA file
[2019-05-08 09:04:21] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:04:26] Reading known junctions from GTF file
[2019-05-08 09:04:31] Preparing reads
	 left reads: min. length=101, max. length=101, 35195209 kept reads (219251 discarded)
[2019-05-08 09:18:49] Building transcriptome data files /scratch/5992727.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:19:08] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:28:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 09:58:10] Resuming TopHat pipeline with unmapped reads
[2019-05-08 09:58:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:11:34] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:13:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:15:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:17:11] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:19:25] Searching for junctions via segment mapping
[2019-05-08 10:34:41] Retrieving sequences for splices
[2019-05-08 10:36:45] Indexing splices
[2019-05-08 10:38:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 10:38:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 10:39:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 10:41:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 10:41:59] Joining segment hits
[2019-05-08 10:45:19] Reporting output tracks
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[2019-05-08 11:09:06] A summary of the alignment counts can be found in /scratch/5992727.1.linga/tophat2/align_summary.txt
[2019-05-08 11:09:06] Run complete: 02:04:45 elapsed