MING

I have the same problem, and tried the code above, but I still can not pass through this permission issue, what is the problem? Thx

Thanks for your quick response. I used WLS to run cnv_facets, I got erro which is exactly the same error mizunokei had before: mkfifo: cannot create fifo './EVT_cnv.csv.gz_201222-012553_384316d79c87/common_all_20180418.1.vcf': Operation not...

Do I need to restart my computer?

I tried, cnv_facets.R -t Plink1_tumor_dupmark.bam -n Plink1_normal_dupmark.bam -vcf common_all_20180418.vcf.gz -o ~/cvn_out/EVT_cnv snp-pileup: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Error in...

Belows are the info: drwxr-xr-x 1 grace grace 4096 Dec 22 00:51 bcftools-1.11-h7c999a4_0 -rw-r--r-- 1 grace grace 844794 Dec 22 00:51 bcftools-1.11-h7c999a4_0.tar.bz2 drwxr-xr-x 1 grace grace 4096 Dec 22 00:30...

Yes, I have done bind and mount for singularity. When I typed `samtools quickcheck N01_01_WG01.bam`, it did not show any output. I think this is due to the samtools version....

1.15.1 version samtools stii does not show any output after run the above command.

I print out the header of my bam: ``` @HD VN:1.6 SO:coordinate @SQ SN:1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128 UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta SP:HUMAN @SQ SN:2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta SP:HUMAN @SQ SN:3 LN:198022430 M5:fdfd811849cc2fadebc929bb925902e5 UR:file:/igo/work/nabors/tools/bwamem2/ref/gr37.fasta SP:HUMAN...

When I run the command, the output is the sample ID