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YeoLab / gscripts

General Use Scripts and Helper functions
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rna_seq_scala fail at rna_editing using hg19 #50

Closed LeenMachine closed 9 years ago

LeenMachine commented 9 years ago 
ERROR 16:00:55,591 FunctionEdge - Error: create_rna_editing_makefile.py  '--bam' '/oasis/tscc/scratch/ljamal
/cardiac/CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg.bam'  '--snpEffDb' 'hg19'  '--snpDb' '/projects/p
s-yeolab/genomes/hg19/snp137.txt.gz'  '--genome' '/projects/ps-yeolab/genomes/hg19/chromosomes/all.fa'  '--f
lipped' 'flipped'  '--outfile' '/oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.s
orted.rg.editing'  && make -j 2 -f /oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.g
z.sorted.rg.editing 
ERROR 16:00:55,610 FunctionEdge - Contents of /oasis/tscc/scratch/ljamal/cardiac/CarD15-2_C02_CGTACTAG-TAGAT
CGC.fastq.gz.sorted.rg.editing.out:
discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH
discarding /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.0.1_2014-08-12/envs/ljamal/bin to PATH
echo "Calculating confidence for CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg_stage1.noSNP" >> CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg.make.out
python /home/yeo-lab/software/RNA_editing/rankEdits.py CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg_stage1.noSNP 5 5 0.1 0 > CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg_stage1.conf
wc CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg_stage1.conf >> CarD15-2_C02_CGTACTAG-TAGATCGC.fastq.gz.sorted.rg.make.out
olgabot commented 9 years ago

unless @boyko- does this, this won't get fixed in the near future