[Sat Apr 25 01:11:34 2020] Beginning TopHat run (v1.4.1)
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[Sat Apr 25 01:11:34 2020] Preparing output location KO_IL4_replicate_IIb/
[Sat Apr 25 01:11:34 2020] Checking for Bowtie index files
[Sat Apr 25 01:11:34 2020] Checking for reference FASTA file
	Warning: Could not find FASTA file /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/bowtie/mm10.fa
[Sat Apr 25 01:11:34 2020] Reconstituting reference FASTA file from Bowtie index
Executing: /data/results/tools/align/bowtie-0.12.9/bowtie-inspect /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/bowtie/mm10 > KO_IL4_replicate_IIb/tmp/mm10.fa
[Sat Apr 25 01:13:25 2020] Checking for Bowtie
	Bowtie version:			 0.12.9.0
[Sat Apr 25 01:13:25 2020] Checking for Samtools
	Samtools Version: 0.1.19
[Sat Apr 25 01:13:25 2020] Generating SAM header for /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/bowtie/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[Sat Apr 25 01:13:27 2020] Reading known junctions from GTF file
[Sat Apr 25 01:13:40 2020] Preparing reads
	left reads: min. length=15, count=13317846
Warning: short reads (<20bp) will make TopHat quite slow and take large amount of memory because they are likely to be mapped to too many places
[Sat Apr 25 01:16:13 2020] Creating transcriptome data files..
[Sat Apr 25 01:16:38 2020] Building Bowtie index from mm10b.fa
[Sat Apr 25 01:27:40 2020] Mapping left_kept_reads against transcriptome mm10b with Bowtie 
[Sat Apr 25 01:29:54 2020] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[Sat Apr 25 01:31:05 2020] Resuming TopHat pipeline with unmapped reads
[Sat Apr 25 01:31:05 2020] Mapping left_kept_reads.m2g_um against mm10 with Bowtie 
[Sat Apr 25 01:32:50 2020] Processing bowtie hits
[Sat Apr 25 01:40:21 2020] Mapping left_kept_reads.m2g_um_seg1 against mm10 with Bowtie (1/3)
[Sat Apr 25 01:44:46 2020] Mapping left_kept_reads.m2g_um_seg2 against mm10 with Bowtie (2/3)
[Sat Apr 25 01:48:40 2020] Mapping left_kept_reads.m2g_um_seg3 against mm10 with Bowtie (3/3)
[Sat Apr 25 01:51:04 2020] Searching for junctions via segment mapping
[Sat Apr 25 01:56:38 2020] Retrieving sequences for splices
[Sat Apr 25 01:58:58 2020] Indexing splices
[Sat Apr 25 01:59:10 2020] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie (1/3)
[Sat Apr 25 02:00:24 2020] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie (2/3)
[Sat Apr 25 02:01:46 2020] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie (3/3)
[Sat Apr 25 02:02:49 2020] Joining segment hits
[Sat Apr 25 02:06:41 2020] Reporting output tracks
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Run complete [00:59:04 elapsed]