Issue with OTU making

[bionesiacourse]

Hi There NOt really sure why i got this error when running the clustering process. Can somebody please shed a light on this.

Thanks Aji

RuleException in line 449 of /data/home/awahyu/MetaWorks1.9.4/snakefile_OTU: NameError: The name 'SED' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/init.py", line 136, in run_jobs File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/init.py", line 441, in run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/init.py", line 230, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/init.py", line 156, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/init.py", line 162, in printjob

[terrimporter]

Can you send me your config file too?

T

On Thu., Oct. 14, 2021, 4:53 a.m. bionesiacourse, @.***> wrote:

Hi There NOt really sure why i got this error when running the clustering process. Can somebody please shed a light on this.

Thanks Aji

RuleException in line 449 of /data/home/awahyu/MetaWorks1.9.4/snakefile_OTU: NameError: The name 'SED' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 136, in run_jobs File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 441, in run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 230, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 156, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 162, in printjob

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[bionesiacourse]

Hi Teresita

Thanks so much for responding and this is my config file. I run this following ASV step and stuck in OTU clustering process. Also do you have any idea why ORFfinder spitting this error

ORFfinder: error while loading shared libraries: libuv.so.1: cannot open shared object file: No such file or directory

Aji

On Oct 14, 2021, at 8:20 PM, Teresita M. Porter @.***> wrote:

Can you send me your config file too?

T

On Thu., Oct. 14, 2021, 4:53 a.m. bionesiacourse, @.***> wrote:

Hi There NOt really sure why i got this error when running the clustering process. Can somebody please shed a light on this.

Thanks Aji

RuleException in line 449 of /data/home/awahyu/MetaWorks1.9.4/snakefile_OTU: NameError: The name 'SED' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 136, in run_jobs File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 441, in run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 230, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 156, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 162, in printjob

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[terrimporter]

I can’t seem to open your config file. Can you compress it, and send it as an attachment?

Thanks -t

From: bionesiacourse @.> Reply-To: terrimporter/MetaWorks @.> Date: Thursday, October 14, 2021 at 9:31 AM To: terrimporter/MetaWorks @.> Cc: Teresita Porter @.>, Comment @.***> Subject: Re: [terrimporter/MetaWorks] Issue with OTU making (#2)

Hi Teresita

Thanks so much for responding and this is my config file. I run this following ASV step and stuck in OTU clustering process. Also do you have any idea why ORFfinder spitting this error

ORFfinder: error while loading shared libraries: libuv.so.1: cannot open shared object file: No such file or directory

Aji

On Oct 14, 2021, at 8:20 PM, Teresita M. Porter @.***> wrote:

Can you send me your config file too?

T

On Thu., Oct. 14, 2021, 4:53 a.m. bionesiacourse, @.***> wrote:

Hi There NOt really sure why i got this error when running the clustering process. Can somebody please shed a light on this.

Thanks Aji

RuleException in line 449 of /data/home/awahyu/MetaWorks1.9.4/snakefile_OTU: NameError: The name 'SED' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}} File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 136, in run_jobs File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 441, in run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 230, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 156, in _run File "/data/home/awahyu/miniconda3_2018/envs/MetaWorks_v1.9.4/lib/python3.8/site-packages/snakemake/executors/ init.py", line 162, in printjob

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[terrimporter]

I see that you're communicating through github. No need to email the config file. Just tell me which marker you're using?

[bionesiacourse]

CO1

[bionesiacourse]

CO1

On Oct 14, 2021, at 8:42 PM, Teresita M. Porter @.***> wrote:

I see that you're communicating through github. No need to email the config file. Just tell me which marker you're using?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/terrimporter/MetaWorks/issues/2#issuecomment-943370619, or unsubscribe https://github.com/notifications/unsubscribe-auth/ART5TEMXUBWMGDQUVQNYUFDUG3M3NANCNFSM5F7DPR6Q. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[terrimporter]

I've updated MetaWorks to v1.9.5 available here https://github.com/terrimporter/MetaWorks/releases/tag/v1.9.5 This fixes the first problem you reported above with snakefile_OTU and SED.

Run the ESV workflow first: snakemake --jobs 24 --snakefile snakefile_ESV --configfile config_ESV.yaml Then run the OTU workflow: snakemake --jobs 24 --snakefile snakefile_OTU --configfile config_OTU.yaml

Note that you need to update your settings in two separate config files for generating ESVs then for generating the OTUs. I've tested this with the CO1 test data provided in /testing .