No such file or directory: tmpdir/Summary_ReadCount_MmuWvXg.txt

[xiucz]

Hi,
Thanks for your tool.When I try to use the commandline to start the normalize step, it shows the error, and norm-config.txt I have created was erased empty.

$ ~/SVtools/BICseq/NBICseq-norm_v0.2.4/NBICseq-norm.pl --tmp=tmpdir -l 150 -s 150 -p 0.0002 -b 100 BICseqtest/ BICseqtest/norm-config.txt

This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
No such file or directory: tmpdir/Summary_ReadCount_MmuWvXg.txt

Here is my norm-config.txt file.(tab seprated each column)

$ head -n 2 
chromName       faFile  MapFile readPosFile     binFileNorm
chr1    ~/hg19/gatk_bundle/ref_split//chr1.fa ~/hg19/gatk_bundle/mappability/ucsc.hg19.150mer//ucsc.hg19.150mer.chr1.txt        ~/BICseq/SEQ/chr1.seq ~/BICseq/bin/chr1.bin

Can you give me some advice to debug it?
Best,
xiucz

[jgarces02]

Hi @xiucz, were you able to solve this? Thanks

[xiucz]

@jgarces02
Not yet, ichorCNA or CNVpytor may be a good choice.