[2019-05-08 08:18:15] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:18:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:18:16] Checking for Bowtie index files (genome)..
[2019-05-08 08:18:16] Checking for reference FASTA file
[2019-05-08 08:18:16] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:18:20] Reading known junctions from GTF file
[2019-05-08 08:18:28] Preparing reads
	 left reads: min. length=101, max. length=101, 34272289 kept reads (217664 discarded)
[2019-05-08 08:38:49] Building transcriptome data files /scratch/5992720.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:39:24] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:52:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 09:24:43] Resuming TopHat pipeline with unmapped reads
[2019-05-08 09:24:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 09:47:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 09:49:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 09:51:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 09:54:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 09:56:52] Searching for junctions via segment mapping
[2019-05-08 10:01:33] Retrieving sequences for splices
[2019-05-08 10:03:45] Indexing splices
[2019-05-08 10:05:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 10:05:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 10:06:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 10:06:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 10:07:21] Joining segment hits
[2019-05-08 10:12:46] Reporting output tracks
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[2019-05-08 10:47:16] A summary of the alignment counts can be found in /scratch/5992720.1.linga/tophat2/align_summary.txt
[2019-05-08 10:47:16] Run complete: 02:29:00 elapsed