[2019-05-08 08:10:05] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:10:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:10:06] Checking for Bowtie index files (genome)..
[2019-05-08 08:10:06] Checking for reference FASTA file
[2019-05-08 08:10:06] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:10:10] Reading known junctions from GTF file
[2019-05-08 08:10:20] Preparing reads
	 left reads: min. length=101, max. length=101, 33813204 kept reads (341052 discarded)
[2019-05-08 08:22:39] Building transcriptome data files /scratch/5992718.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:22:57] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:31:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 08:50:43] Resuming TopHat pipeline with unmapped reads
[2019-05-08 08:50:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 09:04:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 09:06:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 09:10:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 09:13:51] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 09:15:46] Searching for junctions via segment mapping
[2019-05-08 09:20:19] Retrieving sequences for splices
[2019-05-08 09:22:48] Indexing splices
[2019-05-08 09:23:30] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:23:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:24:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:24:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:25:15] Joining segment hits
[2019-05-08 09:28:39] Reporting output tracks
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[2019-05-08 09:44:46] A summary of the alignment counts can be found in /scratch/5992718.1.linga/tophat2/align_summary.txt
[2019-05-08 09:44:46] Run complete: 01:34:40 elapsed