Problem running the anvi-filter-sqm.py script SMQ2anvio

[apazminov]

Hello, I am having issues running the anvi-filter-sqm.py script, the previous script (anvi-load-sqm.py) ran succesfully and the CONTIGS.db, PROFILE.db and Taxonomy.txt were created. The issue is as follows:

Config Error: Something went wrong during subsetting :/ Table names in the parent db (/home/bi otechlab/2TB_2/Proyecto_Almohadillas/Samples/Squeezemeta/Squeezemeta_Almohadilla s2/anvio/antibiotic_YOLO/CONTIGS.db) and the child db (/home/biotechlab/2TB_2/Pr oyecto_Almohadillas/Samples/Squeezemeta/Squeezemeta_Almohadillas2/anvio/antibiot ic/SqueezeMeta/CONTIGS.db) does not seem to be identical. The following tables
are found in the source, but missing in the target database: '' Running anvi-interactive with: anvi-interactive -c /home/biotechlab/2TB_2/Proyecto_Almohadillas/Samples/Squeezemeta/Squeezemeta_Almohadillas2/anvio/antibiotic/SqueezeMeta/CONTIGS.db -p /home/biotechlab/2TB_2/Proyecto_Almohadillas/Samples/Squeezemeta/Squeezemeta_Almohadillas2/anvio/antibiotic/SqueezeMeta/PROFILE.db -t /home/biotechlab/2TB_2/Proyecto_Almohadillas/Samples/Squeezemeta/Squeezemeta_Almohadillas2/anvio/antibiotic/Taxonomy.nwk Contigs DB ...................................: Initialized:
/home/biotechlab/2TB_2/Proyecto_Almohadillas/Samples/Squeezemeta/Squeezemeta_Almohadillas2/anvio/antibiotic/SqueezeMeta/CONTIGS.db (v. 21) Splits taxonomy ..............................: Initiated for taxonomic level for "t_genus"

Config Error: There is nothing at '/home/biotechlab/2TB_2/Proyecto_Almohadillas/Samples/Squeez emeta/Squeezemeta_Almohadillas2/anvio/antibiotic/SqueezeMeta/PROFILE.db' :/

I didn't find any previous thread related to this issue, if you could please help me with this? The packages specifications are as follows: SQMtools_1.6.3 anvio-8 SqueezeMeta 1.6.3

Thank you, Miguel

[fpusan]

Probably because you are using anvio v8, as our last supported version is anvio v7.

I can confirm anvi-filter-sqm.py works for me with anvio v7 and the latest SqueezeMeta release.

However the anvio7 conda package didn't work out of the box and I had to fiddle around with several package versions in order to get anvi-self-test working, Even after doing that, I needed to downgrade the mistune package to version 0.8 in order to make everything work.

[apazminov]

Hello Fernando,

Thanks for the quick response! I am trying to install anvio v7 following the steps in the anvio installation page but with v7. But I am having problems installing anvio with pip as there are problems builidng the wheels for pandas due to some deprecated packages (pkg_resources is deprecated). If you could please let me know how you were able to install it, it would be really helpful.

Thanks again!

Miguel

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From: Fernando Puente-Sánchez @.> Sent: Tuesday, December 19, 2023 7:15 AM To: jtamames/SqueezeMeta @.> Cc: Miguel Pazmiño Vela @.>; Author @.> Subject: Re: [jtamames/SqueezeMeta] Problem running the anvi-filter-sqm.py script SMQ2anvio (Issue #763)

Probably because you are using anvio v8, as our last supported version is anvio v7.

I can confirm anvi-filter-sqm.py works for me with anvio v7 and the latest SqueezeMeta release.

However the anvio7 conda package didn't work out of the box and I had to fiddle around with several package versions in order to get anvi-self-test working, Even after doing that, I needed to downgrade the mistune package to version 0.8 in order to make everything work.

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/jtamames/SqueezeMeta/issues/763*issuecomment-1862651418__;Iw!!NN-i7gBg!txscxhree7qjL-BS3yJOUtQFsvZNCVI39eQF61HKLUjmy2OMPx3p4h1kzVFN-NRJDNNAA5cIJ8ah-lE-yJGsM4hK74pXOA$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BEWMN6AGGV2YUNC6FOAB3G3YKGANPAVCNFSM6AAAAABAWSWDFKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRSGY2TCNBRHA__;!!NN-i7gBg!txscxhree7qjL-BS3yJOUtQFsvZNCVI39eQF61HKLUjmy2OMPx3p4h1kzVFN-NRJDNNAA5cIJ8ah-lE-yJGsM4ihHlmAVg$. You are receiving this because you authored the thread.Message ID: @.***>

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[http://www4.usfq.edu.ec/owa/logo_usfq.png] Miguel Pazmiño Vela Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito T: (+593) 2 297-1700 ext. Correo: @.*** Diego de Robles y Vía Interoceánica, Quito, Ecuador http://www.usfq.edu.ec Nota de descargo: La información contenida en éste e-mail es confidencial y sólo puede ser utilizada por el individuo o la institución a la cual está dirigido. Esta información no debe ser distribuida ni copiada total o parcialmente por ningún medio sin la autorización de la USFQ. La institución no asume responsabilidad sobre información, opiniones o criterios contenidos en este mail que no estén relacionados con asuntos oficiales de nuestra institución. Disclaimer: The information in this e-mail is confidential and intended only for the use of the person or institution to which it is addressed. This information is considered provisional and referential; it cannot be totally or partially distributed nor copied by any media without authorization from USFQ. The institution does not assume responsibility about the information, opinions or criteria in this e-mail.

[fpusan]

I started from the bioconda anvio7 package version but then I had to manually update/downgrade several packages until I made It work. I'm many cases I couldn't do It from conda so I used pip instead (but inside the conda environment, of course) Sorry I can not provide more details, I didn't document the process. If you still can not manage maybe you can ask the anvio people...

[apazminov]

No problem,

Thanks again for all the help!

Greetings, Miguel

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From: Fernando Puente-Sánchez @.> Sent: Tuesday, December 19, 2023 12:28 PM To: jtamames/SqueezeMeta @.> Cc: Miguel Pazmiño Vela @.>; Author @.> Subject: Re: [jtamames/SqueezeMeta] Problem running the anvi-filter-sqm.py script SMQ2anvio (Issue #763)

I started from the bioconda anvio7 package version but then I had to manually update/downgrade several packages until I made It work. I'm many cases I couldn't do It from conda so I used pip instead (but inside the conda environment, of course) Sorry I can not provide more details, I didn't document the process. If you still can not manage maybe you can ask the anvio people...

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/jtamames/SqueezeMeta/issues/763*issuecomment-1863200784__;Iw!!NN-i7gBg!qvgCMm6PETovhzxqBfhQkQX-i5sc9PwXtZtzCL4SPFVA55PP-9dFSHjaRRraMAMdbpOLc0lCk3tg6xAz0gZxgFUNBE8_iw$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BEWMN6HMW3DTW22M4XTGPZTYKHFD7AVCNFSM6AAAAABAWSWDFKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRTGIYDANZYGQ__;!!NN-i7gBg!qvgCMm6PETovhzxqBfhQkQX-i5sc9PwXtZtzCL4SPFVA55PP-9dFSHjaRRraMAMdbpOLc0lCk3tg6xAz0gZxgFXlTKkmUg$. You are receiving this because you authored the thread.Message ID: @.***>

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[http://www4.usfq.edu.ec/owa/logo_usfq.png] Miguel Pazmiño Vela Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito T: (+593) 2 297-1700 ext. Correo: @.*** Diego de Robles y Vía Interoceánica, Quito, Ecuador http://www.usfq.edu.ec Nota de descargo: La información contenida en éste e-mail es confidencial y sólo puede ser utilizada por el individuo o la institución a la cual está dirigido. Esta información no debe ser distribuida ni copiada total o parcialmente por ningún medio sin la autorización de la USFQ. La institución no asume responsabilidad sobre información, opiniones o criterios contenidos en este mail que no estén relacionados con asuntos oficiales de nuestra institución. Disclaimer: The information in this e-mail is confidential and intended only for the use of the person or institution to which it is addressed. This information is considered provisional and referential; it cannot be totally or partially distributed nor copied by any media without authorization from USFQ. The institution does not assume responsibility about the information, opinions or criteria in this e-mail.