Error: Failed to open data.vcf.gz. (--vcf expects a complete filename; did you forget '.vcf' at the end?)

[jaisonjseq]

Hi.

I am an absolute beginner in this aspect. When I run the script with a vcf input file, I get this error. Error: Failed to open data.vcf.gz. (--vcf expects a complete filename; did you forget '.vcf' at the end?)

.vcf file location is correct. I tried with the compressed vcf.gz as well. It returns the same error. Files are attached.

configfile.txt
test_hapne.txt
data: https://1drv.ms/t/s!AqI0TE_dbYRRg1nZ3uQAcPPqNYkU?e=mvz2kW

Eagerly looking forward to your response.

[rmnfournier]

Hi!

The file "data" you shared seems to have a .txt extension instead of .vcf.gz.
Is there a file called data.vcf.gz in your directory when you call the script?
You can probably do something like:
mv data.txt data.vcf
Followed by:
gzip data.vcf
To obtain the file in the correct format.

If there is indeed a vcf.gz file in the directory and the .txt was just there to share the file, you might want to try with the absolute path to your data as input.

I hope this helps!

[jaisonjseq]

Hi! Thank you for your swift response. The earlier issue has been resolved using gzip data.vcf. Now, I get this error message: plink: unknown option "--make-bed" plink: unknown option "--out" plink: unknown option "--vcf" plink: unknown option "--make-bed" plink: unknown option "--out" plink: unknown option "--vcf" plink: unknown option "--make-bed" plink: unknown option "--out" Traceback (most recent call last): File "/home/jaison/HapNe/test_hapne.py", line 20, in <module> compute_ld(config) File "/home/jaison/miniconda3/lib/python3.11/site-packages/hapne/ld.py", line 45, in compute_ld compute_ld_in_parallel(ii, config) File "/home/jaison/miniconda3/lib/python3.11/site-packages/hapne/ld.py", line 71, in compute_ld_in_parallel genotype, chr_map = load_and_preprocess_file(genotype_folder + "/" + region["NAME"] + ".bed", ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/jaison/miniconda3/lib/python3.11/site-packages/hapne/ld.py", line 215, in load_and_preprocess_file genotype, chr_map = load_files(bed_file) ^^^^^^^^^^^^^^^^^^^^ File "/home/jaison/miniconda3/lib/python3.11/site-packages/hapne/ld.py", line 329, in load_files genotype_object = pdp.read_plink1_bin(prefix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/jaison/miniconda3/lib/python3.11/site-packages/pandas_plink/_read.py", line 265, in read_plink1_bin raise ValueError("No BED file has been found.") ValueError: No BED file has been found. Which BED file is it asking for? Regards, Jaison Sequeira

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On Wed, Feb 28, 2024 at 2:05 PM Romain Fournier ***@***.***> wrote: Hi! The file "data" you shared seems to have a .txt extension instead of .vcf.gz. Is there a file called data.vcf.gz in your directory when you call the script? You can probably do something like: mv data.txt data.vcf Followed by: gzip data.vcf To obtain the file in the correct format. If there is indeed a vcf.gz file in the directory and the .txt was just there to share the file, you might want to try with the absolute path to your data as input. I hope this helps! — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A2H3GUE6ZENP6R55AMTOAO3YV3T6HAVCNFSM6AAAAABDYZHEEGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRYGQ3TMMJUGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[rmnfournier]

Hi,
There seems to be an issue when creating bed files using Plink in the pipeline. Are you using the conda environment provided in the readme file? If yes, could you run the command plink --version in the terminal after activating the environment to make sure that everything has been correctly installed?

[jaisonjseq]

I have followed the steps listed in the readme file. Looks like everything is correctly installed. (HapNe) ***@***.***:~$ plink --version PLINK v1.90b6.21 64-bit (19 Oct 2020) (HapNe) ***@***.***:~$ Regards, Jaison Sequeira

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On Thu, Feb 29, 2024 at 12:19 AM Romain Fournier ***@***.***> wrote: Hi, There seems to be an issue when creating bed files using Plink in the pipeline. Are you using the conda environment provided in the readme file? If yes, could you run the command plink --version in the terminal after activating the environment to make sure that everything has been correctly installed? — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A2H3GUAB3WWFWA7HSUCTWPLYV532ZAVCNFSM6AAAAABDYZHEEGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRZGYZDENZRHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jaisonjseq]

Was the error due to the genetic map file? I used this file now fingerprint_maps/references/genetic_map_hg38.tar.gz at master · naumanjaved/fingerprint_maps (github.com) <https://github.com/naumanjaved/fingerprint_maps/blob/master/references/genetic_map_hg38.tar.gz> The program is now running (image attached). Am I doing it correctly? Regards, Jaison Sequeira On Thu, Feb 29, 2024 at 12:47 AM Jaison J Sequeira ***@***.***> wrote:

…

I have followed the steps listed in the readme file. Looks like everything is correctly installed. (HapNe) ***@***.***:~$ plink --version PLINK v1.90b6.21 64-bit (19 Oct 2020) (HapNe) ***@***.***:~$ Regards, Jaison Sequeira On Thu, Feb 29, 2024 at 12:19 AM Romain Fournier ***@***.***> wrote: > Hi, > There seems to be an issue when creating bed files using Plink in the > pipeline. Are you using the conda environment provided in the readme file? > If yes, could you run the command plink --version in the terminal after > activating the environment to make sure that everything has been correctly > installed? > > — > Reply to this email directly, view it on GitHub > <#1 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/A2H3GUAB3WWFWA7HSUCTWPLYV532ZAVCNFSM6AAAAABDYZHEEGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRZGYZDENZRHA> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >