[2019-05-08 07:58:31] Beginning TopHat run (v2.1.1)
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[2019-05-08 07:58:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 07:58:32] Checking for Bowtie index files (genome)..
[2019-05-08 07:58:32] Checking for reference FASTA file
[2019-05-08 07:58:32] Generating SAM header for Bowtie2Index/genome
[2019-05-08 07:58:36] Reading known junctions from GTF file
[2019-05-08 07:58:40] Preparing reads
	 left reads: min. length=101, max. length=101, 32465301 kept reads (249269 discarded)
[2019-05-08 08:11:16] Building transcriptome data files /scratch/5992717.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:11:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 08:20:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 08:39:27] Resuming TopHat pipeline with unmapped reads
[2019-05-08 08:39:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 08:53:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 08:54:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 08:56:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 08:57:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 08:59:32] Searching for junctions via segment mapping
[2019-05-08 09:04:04] Retrieving sequences for splices
[2019-05-08 09:06:11] Indexing splices
[2019-05-08 09:06:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:07:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:07:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:08:00] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:08:23] Joining segment hits
[2019-05-08 09:11:28] Reporting output tracks
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[2019-05-08 09:30:07] A summary of the alignment counts can be found in /scratch/5992717.1.linga/tophat2/align_summary.txt
[2019-05-08 09:30:07] Run complete: 01:31:35 elapsed