[2019-05-08 09:18:05] Beginning TopHat run (v2.1.1)
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[2019-05-08 09:18:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 09:18:07] Checking for Bowtie index files (genome)..
[2019-05-08 09:18:07] Checking for reference FASTA file
[2019-05-08 09:18:07] Generating SAM header for Bowtie2Index/genome
[2019-05-08 09:18:13] Reading known junctions from GTF file
[2019-05-08 09:18:18] Preparing reads
	 left reads: min. length=101, max. length=101, 39218651 kept reads (321276 discarded)
[2019-05-08 09:39:47] Building transcriptome data files /scratch/5992731.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 09:40:07] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:48:26] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 10:18:12] Resuming TopHat pipeline with unmapped reads
[2019-05-08 10:18:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 10:38:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 10:41:13] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 10:44:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 10:47:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 10:50:44] Searching for junctions via segment mapping
[2019-05-08 11:05:43] Retrieving sequences for splices
[2019-05-08 11:08:00] Indexing splices
[2019-05-08 11:09:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 11:10:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 11:11:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 11:12:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 11:14:03] Joining segment hits
[2019-05-08 11:17:48] Reporting output tracks
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[2019-05-08 11:42:46] A summary of the alignment counts can be found in /scratch/5992731.1.linga/tophat2/align_summary.txt
[2019-05-08 11:42:46] Run complete: 02:24:40 elapsed