mkfifo: cannot create fifo...

[mizunokei]

Hello dariober, I'm trying to run cnv_facets on Ubuntu but it doesn't work. cnv_facets.R -t <tumour.bam> -n <normal.bam> -vcf common_all_20180418.vcf.gz -o <output>

the error message like: mkfifo: cannot create fifo ‘output.csv.gz_200520-155405_29956dc5eb59/common_all_20180418.1.vcf’: Operation not permitted Error in checkForRemoteErrors(val) : one node produced an error: Error in computing snp pileup. Exit code 1 from execution of output.csv.gz_200520-155405_29956dc5eb59/snp_pileup.1.sh Calls: exec_snp_pileup_parallel ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted

Thanks in advance for your reply!

[dariober]

Hi- sorry about that. My first guess is that you don't have permission to write in the directory where you direct the output files. However, cnv_facets seems to have created dir output.csv.gz_200520-155405_29956dc5eb59/ so writing permission shouldn't be a problem. Well, unless permission have changed in the meantime which seems odd.

In the directory where you execute cnv_facets, try to do:

mkdir mytmp
mkfifo mytmp/common_all_20180418.1.vcf

and see what happens.

[mizunokei]

Thank you for your quick reply. I will try and see what happens.

[mizunokei]

Thanks to your comment, I've succeeded in running the program.

I have one more question here: The tumor purity is "NA" in all samples. Why?

Thank you again for your reply.

[gaom001]

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

[dariober]

@gaom001 Can you give me more information? What command did you run and what error message did you get?

[gaom001]

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 permitted Error in checkForRemoteErrors(val) : one node produced an error: Error in computing snp pileup. Exit code 1 from execution of ./EVT_cnv.csv.gz_201222-012553_384316d79c87/snp_pileup.1.sh Calls: exec_snp_pileup_parallel ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted

then I did above code: mkfifo mytmp mkfifo mytmp/common_all_20180418.1.vcf

but still can not operate. mkfifo: cannot create fifo 'mytmp/common_all_20180418.1.vcf': Operation not permitted

Please advise.

[gaom001]

Do I need to restart my computer?

[dariober]

It seems to me that you are trying to write your output in a directory where you don't have permission to write. Try something like:

cnv_facets.R -o ~/cvn_out/EVT_cnv

This will create output files with prefix EVT_cnv inside directory cvn_out in your home directory where you should be able to write.

[gaom001]

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 checkForRemoteErrors(val) : one node produced an error: Error in computing snp pileup. Exit code 127 from execution of /home/grace/cvn_out/EVT_cnv.csv.gz_201222-090249_35b1c193a70/snp_pileup.1.sh Calls: exec_snp_pileup_parallel ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted

Sorry, this is my first time to run this on Linux. Still can not write it out. I am not a CS graduate, lol...

[dariober]

snp-pileup: error while loading shared libraries: libcrypto.so.1.0.0

This suggests that, at least, you passed the permission error from before. It suggests that snp-pileup is not properly installed. How did you install cnv_facets? And what version of bcftools do you have? Executing bcftools -v should return version 1.9 or higher.

[gaom001]

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 bcftools-1.9-ha228f0b_4

drwxr-xr-x 1 grace grace 4096 Dec 22 00:51 cnv_facets-0.15.0-r36h516909a_0 -rw-r--r-- 1 grace grace 210317742 Dec 22 00:51 cnv_facets-0.15.0-r36h516909a_0.tar.bz2 drwxr-xr-x 1 grace grace 4096 Dec 22 00:32 cnv_facets-0.16.0-py38r36h4b26f60_1 -rw-r--r-- 1 grace grace 210314152 Dec 22 00:32 cnv_facets-0.16.0-py38r36h4b26f60_1.tar.bz2

I failed to install cnv_facets intially, the system was solving environment... then found this pkgs, then installed.

What should I do o fix this issue? many thanks again

[dariober]

Have you tried installing in a separate conda envirnoment? E.g. using:

conda create -n cnv_facets
conda activate cnv_facets
conda install -c bioconda -c conda-forge cnv_facets 

Do any of these commands return an errror?