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kensung-lab / INSurVeyor

An insertion caller for Illumina paired-end WGS data.
GNU General Public License v3.0
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[E::hts_open_format] Failed to open file #23

Open Myno-Jeong opened 4 months ago

Myno-Jeong commented 4 months ago

Hi, Thank you for making INSurVeyor program. Unfortunately, when I ran this program, the following problem occurred.

Remapping DC for chr4_GL000008v2_random DC remapped in 6 [s] Executing: /home/users/mhjeong/miniconda3/envs/insurveyor-env/bin/add_filtering_info [E::hts_open_format] Failed to open file "INSurVeyor/wrk_space/assembled_ins.vcf.gz" : No such file or directory"

I installed INSurVeyor using miniconda (version: 23.3.1) and I checked the version of installed htslib (version: 1.16). I think you updated INsurVeyor and htslib version (1.16 -> 1.19.1) Also, I checked small_ins.vcf.gz is created.

About setting of INSurVeyor using Docker, I think you have to update dockerfile for installing INSurVeyor without error messages. In dockerfile, htslib used version 1.16. but, you have provided version 1.19.1.

Would you let me know how I solve this problem?

Thank you, best regards,

kp2657 commented 1 week ago

Hi, I was wondering how you solved this as I am encountering the same issue. Thanks!

Mesh89 commented 3 days ago

Hi,

Is the dataset you are using publicly available? Would it be possible for me to try it?

kp2657 commented 3 days ago

Hi, the data isn't publicly available, but I can provide access over email.

On Wed, Nov 27, 2024 at 4:59 AM Mesh89 @.***> wrote:

Hi,

Is the dataset you are using publicly available? Would it be possible for me to try it?

— Reply to this email directly, view it on GitHub https://github.com/kensung-lab/INSurVeyor/issues/23#issuecomment-2503437318, or unsubscribe https://github.com/notifications/unsubscribe-auth/APCVTQDT5FMVZTIQJLZZVIL2CWJYHAVCNFSM6AAAAABK56FNY2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBTGQZTOMZRHA . You are receiving this because you commented.Message ID: @.***>

Mesh89 commented 2 days ago

That would be helpful. You can add gmail.com to my username.

kp2657 commented 2 days ago

Great, sent!

On Thu, Nov 28, 2024 at 6:04 AM Mesh89 @.***> wrote:

That would be helpful. You can add gmail.com to my username.

— Reply to this email directly, view it on GitHub https://github.com/kensung-lab/INSurVeyor/issues/23#issuecomment-2505848188, or unsubscribe https://github.com/notifications/unsubscribe-auth/APCVTQFJCZPJMUCC25QQCQD2C32DLAVCNFSM6AAAAABK56FNY2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBVHA2DQMJYHA . You are receiving this because you commented.Message ID: @.***>