[2019-05-08 08:55:17] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:55:17] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:55:18] Checking for Bowtie index files (genome)..
[2019-05-08 08:55:18] Checking for reference FASTA file
[2019-05-08 08:55:18] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:55:23] Reading known junctions from GTF file
[2019-05-08 08:55:27] Preparing reads
	 left reads: min. length=101, max. length=101, 34161289 kept reads (227070 discarded)
[2019-05-08 09:08:43] Building transcriptome data files /scratch/5992726.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:09:03] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:17:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 09:44:16] Resuming TopHat pipeline with unmapped reads
[2019-05-08 09:44:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:02:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:03:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:05:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:07:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:09:07] Searching for junctions via segment mapping
[2019-05-08 10:21:45] Retrieving sequences for splices
[2019-05-08 10:23:56] Indexing splices
[2019-05-08 10:25:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 10:25:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 10:26:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 10:27:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 10:28:29] Joining segment hits
[2019-05-08 10:31:42] Reporting output tracks
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[2019-05-08 10:56:43] A summary of the alignment counts can be found in /scratch/5992726.1.linga/tophat2/align_summary.txt
[2019-05-08 10:56:43] Run complete: 02:01:25 elapsed