Closed dvmbtk closed 1 year ago
Hi Taylan,
Thanks for the bug report. I will update the tutorial in the next release.
The samplesheet file looks good. Could you run the following command and paste the output here,
cat /home/user/viroprofiler/work/53/fb8743d6315da0b7d868dd3ef9346f/.command.log
Hello,
Here is the output of the above command:
INFO: Converting SIF file to temporary sandbox... WARNING: Skipping mount /home/user/miniconda3/envs/viroprofiler/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [CRITICAL] The given sample sheet does not appear to contain a header. INFO: Cleaning up image...
Best, Taylan
B. Taylan KOÇ, DVM, MSc, PhD Adnan Menderes University Faculty of Veterinary Medicine Department of Virology 09016 Isikli-Aydin/TURKEY Tel. +90 256 247 07 00 / 6204 Mail: @. @.>, @.***
On Wed, Apr 12, 2023 at 7:45 PM Jinlong Ru @.***> wrote:
Hi Taylan,
Thanks for the bug report. I will update the tutorial in the next release.
The samplesheet file looks good. Could you run the following command and paste the output here,
cat /home/user/viroprofiler/work/53/fb8743d6315da0b7d868dd3ef9346f/.command.log
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-- Aydın Adnan Menderes Üniversitesi GIZLILIK NOTU: Bu mesaj ve ekleri yalnizca gönderildigi kisi(lere) ozeldir ve gizlidir. Mesaj sizin adiniza degilse, içerigini ve varsa ekindeki dosyalari kimseye göndermeyiniz ya da kopyalamayiniz. Bu mesajin herhangi bir sekilde açiklanmasi, kullanilmasi, kopyalanmasi, yayilmasi veya mesaj içerigi ile ilgili olarak herhangi bir islem yapilmasi kesinlikle yasaktir. Böyle bir durumda lütfen göndereni uyarip, mesaji siliniz. Aydın Adnan Menderes Üniversitesi bu mesajin içerigi ve ekleri ile ilgili olarak hiçbir hukuksal sorumlulugu kabul etmez.
I guess the error is caused by singularity. Did you install singularity using root or conda? What is the version and path of installed singularity?
Hello, I installed using conda. Version 3.8.6.
B. Taylan KOÇ, DVM, MSc, PhD Adnan Menderes University Faculty of Veterinary Medicine Department of Virology 09016 Isikli-Aydin/TURKEY Tel. +90 256 247 07 00 / 6204 Mail: @. @.>, @.***
On Fri, Apr 14, 2023 at 1:15 PM Jinlong Ru @.***> wrote:
I guess the error is caused by singularity. Did you install singularity using root or conda? What is the version and path of installed singularity?
— Reply to this email directly, view it on GitHub https://github.com/deng-lab/viroprofiler/issues/2#issuecomment-1508351591, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5VR67RTFBPECVAYUUBW443XBEWTPANCNFSM6AAAAAAW3W65NU . You are receiving this because you authored the thread.Message ID: @.***>
-- Aydın Adnan Menderes Üniversitesi GIZLILIK NOTU: Bu mesaj ve ekleri yalnizca gönderildigi kisi(lere) ozeldir ve gizlidir. Mesaj sizin adiniza degilse, içerigini ve varsa ekindeki dosyalari kimseye göndermeyiniz ya da kopyalamayiniz. Bu mesajin herhangi bir sekilde açiklanmasi, kullanilmasi, kopyalanmasi, yayilmasi veya mesaj içerigi ile ilgili olarak herhangi bir islem yapilmasi kesinlikle yasaktir. Böyle bir durumda lütfen göndereni uyarip, mesaji siliniz. Aydın Adnan Menderes Üniversitesi bu mesajin içerigi ve ekleri ile ilgili olarak hiçbir hukuksal sorumlulugu kabul etmez.
Do you have any other container platform installed on your HPC using root? For example, charliecloud. or ask your sys-admin to install singularity using root?
As far as I know, no other container, including charliecloud, was installed but I am not sure. As you said, I will ask our admin. If problem persists, I will let you know
B. Taylan KOÇ, DVM, MSc, PhD Adnan Menderes University Faculty of Veterinary Medicine Department of Virology 09016 Isikli-Aydin/TURKEY Tel. +90 256 247 07 00 / 6204 Mail: @. @.>, @.***
On Fri, Apr 14, 2023 at 1:52 PM Jinlong Ru @.***> wrote:
Do you have any other container platform installed on your HPC using root? For example, charliecloud. or ask your sys-admin to install singularity using root?
— Reply to this email directly, view it on GitHub https://github.com/deng-lab/viroprofiler/issues/2#issuecomment-1508389109, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5VR67QKEPTBVLNYELVQALLXBE3BRANCNFSM6AAAAAAW3W65NU . You are receiving this because you authored the thread.Message ID: @.***>
-- Aydın Adnan Menderes Üniversitesi GIZLILIK NOTU: Bu mesaj ve ekleri yalnizca gönderildigi kisi(lere) ozeldir ve gizlidir. Mesaj sizin adiniza degilse, içerigini ve varsa ekindeki dosyalari kimseye göndermeyiniz ya da kopyalamayiniz. Bu mesajin herhangi bir sekilde açiklanmasi, kullanilmasi, kopyalanmasi, yayilmasi veya mesaj içerigi ile ilgili olarak herhangi bir islem yapilmasi kesinlikle yasaktir. Böyle bir durumda lütfen göndereni uyarip, mesaji siliniz. Aydın Adnan Menderes Üniversitesi bu mesajin içerigi ve ekleri ile ilgili olarak hiçbir hukuksal sorumlulugu kabul etmez.
Description of the bug
Hello,
We are trying out the pipeline, the setup went ok. One note: the parameters for the "mode" option were not in the tutorial, but we found it when we tried running it.
Currently we are getting the below error at the first step of checking the samplesheet.
The samplesheet is also attached and appears to be the right format but perhaps we missed something.
Any advice is appreciated. Thank you in advance.
Best, Taylan & Nori
Command used and terminal output
Relevant files
sample,fastq_1,fastq_2 no131-0_2017,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no131-0_2017_R1_trimmed.fastq.gz,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no131-0_2017_R2_trimmed.fastq.gz no132-0_2017,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no132-0_2017_R1_trimmed.fastq.gz,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no132-0_2017_R2_trimmed.fastq.gz no133-1_2017,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no133-1_2017_R1_trimmed.fastq.gz,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no133-1_2017_R2_trimmed.fastq.gz
System information