command not found

[WUD2018]

Hey developer,

Thanks for your contribution, I have installed the BASALT via conda. However, when I enter the environment, and type 'BASALT', the system reads; BASALT: command not found

Should I add it to the PATH? if so, by how, please let me know, thanks.

Here is my installation process:

git clone https://github.com/EMBL-PKU/BASALT.git cd ./BASALT chmod -R 755 ./ mamba env create -n BASALT --file basalt_env.yml

[Ma-Yingxue]

I just had the very same question, even with all three installation methods. Have you downloaded successfully?

[WUD2018]

Yes, all the packages have been successfully downloaded and installed (you may see my attached pics).

I tried conda and setup.py and none of them works.

[EMBL-PKU]

I am not sure what happened. Did you try BASALT -h? Could you please try this command? If there is still a problem, it would be the problem from installation. We need to check this.

[WUD2018]

Yes, I have tried -h and --help. Still the same problem. 'BASALT: command not found'

[zfsh]

I met the same trouble too, I wonder have you solved this problem? And how do you solve it, thanks.

[WUD2018]

not yet, still awaits the developer's feedback

[EMBL-PKU]

Hi, you need to put the BASALT_script.zip into your system. Please check whether this step has been done. If there is any question, please let me know. Best,

[EMBL-PKU]

There is no BASALT command in the PATH for that environment (e.g. .conda/env/BASALT/bin). You may be able to solve this by manually unzipping BASALT/BASALT_script.zip and changing the permissions on BASALT/BASALT_script/BASALT.

[WUD2018]

There is no BASALT command in the PATH for that environment (e.g. .conda/env/BASALT/bin). You may be able to solve this by manually unzipping BASALT/BASALT_script.zip and changing the permissions on BASALT/BASALT_script/BASALT.

Hello there,

I have done the same as you suggested, but it still did not work as we expected.

However, when I type the absolute path of BALST it seems to give some positive feedback.

So, I still need to put the path of the script PATH in .bashrc

Thanks for your efforts and development of this software.

hope this comment can also help others.

[EMBL-PKU]

Thank you for your patient and support for BASALT. We are going to make this software better. Please let me know if there is any questions. We may also send an email to me in case sometimes I did not read the issue page. My email is yuke.sz@pku.edu.cn

[WUD2018]

Dear developer,

Here is the issue, seems like the installation did not create a path in .cache? How can I solve it? Thanks.

Processing assemblies: ['FC.lm.SwabRes.Sum.hrm.contigs.fa', 'FC.zl.SwabRes.Sum.hrm.contigs.fa', 'KC.hyq.SwabRes.Sum.hrm.contigs.fa', 'KC.xys.SwabRes.Sum.hrm.contigs.fa', 'LR.cz.SwabRes.Sum.hrm.contigs.fa', 'LR.hml.SwabRes.Sum.hrm.contigs.fa', 'LR.wbk.SwabRes.Sum.hrm.contigs.fa', 'LR.wmj.SwabRes.Sum.hrm.contigs.fa', 'LR.wny.SwabRes.Sum.hrm.contigs.fa', 'LR.wxn.SwabRes.Sum.hrm.contigs.fa', 'LR.zzf.SwabRes.Sum.hrm.contigs.fa', 'SB.hfl.SwabRes.Sum.hrm.contigs.fa', 'SB.lwh.SwabRes.Sum.hrm.contigs.fa', 'SB.slh.SwabRes.Sum.hrm.contigs.fa', 'TW.cy.SwabRes.Sum.hrm.contigs.fa', 'TW.cyz.SwabRes.Sum.hrm.contigs.fa', 'TW.djc.SwabRes.Sum.hrm.contigs.fa', 'TW.lcb.SwabRes.Sum.hrm.contigs.fa'] Processing short-reads: {'1': ['FC.lm.SwabRes.Sum.hrm_1.fq', 'FC.lm.SwabRes.Sum.hrm_2.fq'], '2': ['FC.zl.SwabRes.Sum.hrm_1.fq', 'FC.zl.SwabRes.Sum.hrm_2.fq'], '3': ['KC.hyq.SwabRes.Sum.hrm_1.fq', 'KC.hyq.SwabRes.Sum.hrm_2.fq'], '4': ['KC.xys.SwabRes.Sum.hrm_1.fq', 'KC.xys.SwabRes.Sum.hrm_2.fq'], '5': ['LR.cz.SwabRes.Sum.hrm_1.fq', 'LR.cz.SwabRes.Sum.hrm_2.fq'], '6': ['LR.hml.SwabRes.Sum.hrm_1.fq', 'LR.hml.SwabRes.Sum.hrm_2.fq'], '7': ['LR.wbk.SwabRes.Sum.hrm_1.fq', 'LR.wbk.SwabRes.Sum.hrm_2.fq'], '8': ['LR.wmj.SwabRes.Sum.hrm_1.fq', 'LR.wmj.SwabRes.Sum.hrm_2.fq'], '9': ['LR.wny.SwabRes.Sum.hrm_1.fq', 'LR.wny.SwabRes.Sum.hrm_2.fq'], '10': ['LR.wxn.SwabRes.Sum.hrm_1.fq', 'LR.wxn.SwabRes.Sum.hrm_2.fq'], '11': ['LR.zzf.SwabRes.Sum.hrm_1.fq', 'LR.zzf.SwabRes.Sum.hrm_2.fq'], '12': ['SB.hfl.SwabRes.Sum.hrm_1.fq', 'SB.hfl.SwabRes.Sum.hrm_2.fq'], '13': ['SB.lwh.SwabRes.Sum.hrm_1.fq', 'SB.lwh.SwabRes.Sum.hrm_2.fq'], '14': ['SB.slh.SwabRes.Sum.hrm_1.fq', 'SB.slh.SwabRes.Sum.hrm_2.fq'], '15': ['TW.cy.SwabRes.Sum.hrm_1.fq', 'TW.cy.SwabRes.Sum.hrm_2.fq'], '16': ['TW.cyz.SwabRes.Sum.hrm_1.fq', 'TW.cyz.SwabRes.Sum.hrm_2.fq'], '17': ['TW.djc.SwabRes.Sum.hrm_1.fq', 'TW.djc.SwabRes.Sum.hrm_2.fq'], '18': ['TW.lcb.SwabRes.Sum.hrm_1.fq', 'TW.lcb.SwabRes.Sum.hrm_2.fq']} Processing long-reads: [] Processing hifi-reads: [] Processing Hi-C reads: [] Process with extra binner: [] Quality check software: checkm Processing with: 90 threads Processing with: 550 G Running status: continue Binning module: all Min completeness: 50 Max contamination: 10 Autobinning parameter: more-sensitive Refinement parameter: deep Traceback (most recent call last): File "/home/dell/ToolsBin/BASALT/BASALT_script/BASALT", line 141, in BASALT_main_c(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, autobining_parameters, refinement_paramter, max_ctn, min_cpn, pwd, QC_software) File "/home/dell/ToolsBin/BASALT/BASALT_script/BASALT_main_c.py", line 30, in BASALT_main_c os.chdir(local_dir) FileNotFoundError: [Errno 2] No such file or directory: '/home/dell/.cache/BASALT'

---

武冬 D. WU, PhD 华东师范大学生态与环境学学学院 Research Fellow Zijiang Young Scholar School of Ecological and Environmental Science East China Normal University Shanghai, China

https://www.researchgate.net/profile/Dong_Wu25 https://faculty.ecnu.edu.cn/_s31/wd2_en_19490/main.psp

On 4/5/2024 @.***> wrote：

Thank you for your patient and support for BASALT. We are going to make this software better. Please let me know if there is any questions. We may also send an email to me in case sometimes I did not read the issue page. My email is @. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.>

[B1991ing]

FileNotFoundError: [Errno 2] No such file or directory: '/home/dell/.cache/BASALT'

Hi,

How do you finally solve the issue - FileNotFoundError: [Errno 2] No such file or directory: '/home/dell/.cache/BASALT'?

Best,

Bing