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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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External database #658

Closed lisiruisusan closed 1 year ago

lisiruisusan commented 1 year ago

Dear author,

I came up with a problem when adding new database to existing projects. What shall I do?

(SqueezeMeta) zzzhou@dell-PowerEdge-R740:~$ add_database.pl /database/users/zzzhou/huichen/Hadza /database/users/zzzhou/phi.dmnd

add_database.pl - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

This is part of the SqueezeMeta distribution (https://github.com/jtamames/SqueezeMeta) Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 10.3389 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

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Error: Invalid parameter count for option '--db' Error running command: /database/users/zzzhou/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/diamond blastp -q /database/users/zzzhou/huichen/Hadza/results/03.Hadza.faa -p 12 -d -e 0.001 --id 30 --quiet -b NF -f 6 qseqid qlen sseqid slen pident length evalue bitscore qstart qend sstart send -o /database/users/zzzhou/huichen/Hadza/intermediate/04.Hadza.m앤╃󈿗½B0M5l¶g¥whYǿ

.diamond at /database/users/zzzhou/miniconda3/envs/SqueezeMeta/bin/add_database.pl line 71, line 0.000000. (SqueezeMeta) zzzhou@dell-PowerEdge-R740:~$

Yours sincerely,

Li

March 31st 2023

jtamames commented 1 year ago

Hello Please check the manual to find out the correct way of specifying new databases Best,

lisiruisusan commented 1 year ago

Dear author,

Thanks so much for your reply. Problems solved.

Yours sincerely,

Li

March 31st 2023

Panda-smile commented 5 months ago

Hello, I would like to ask how to solve this problem? I've encountered it too, but I don't know what's wrong~

db.list：CazyDB /public/home/zhanglj/squeezemetatrans/Squeezemetacazy /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/CAZyDB.Annotation

run：/public/home/zhanglj/miniconda3/envs/squeezeMeta/SqueezeMeta/utils/add_database.pl shotguntrans db.list

jtamames commented 5 months ago

Please follow the instructions in the manual

Panda-smile commented 5 months ago

Please follow the instructions in the manual

sadly, Professor, still can't run successfully，

(squeezeMeta) [zhanglj@admin Squeezemetacazy]$ ls CAZy_description.txt CAZy.dmnd (squeezeMeta) [zhanglj@admin Squeezemetacazy]$ pwd /public/home/zhanglj/squeezemetatrans/Squeezemetacazy

CazyDB /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/CAZy /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/CAZy_description.txt（db.list）

/public/home/zhanglj/miniconda3/envs/squeezeMeta/SqueezeMeta/utils/add_database.pl shotguntrans db.list（command）

Calculating coverage for functions Can't open EXTDB file CazyDB Can't open EXTDB file CazyDB

jtamames commented 5 months ago

Did you format the database? What is its name?

Panda-smile commented 5 months ago

  1. yes i formatted, its named CAZy.dmnd（Already formatted according to the instructions） /public/home/zhanglj/miniconda3/envs/squeezeMeta/SqueezeMeta/bin/diamond makedb -d /public/home/zhanglj/db/Squeezemetacazy/cazy.dmnd --in /public/home/zhanglj/db/dbcan3/CAZyDB.07262023.fa

  2. or you may mean this database? (squeezeMeta) [zhanglj@admin db]$ ls arc.all.faa bac.scg.faa hmms mito.hmm silva.nr_v132.align arc.hmm bac.scg.lookup hmms_ssu nr.dmnd silva.nr_v132.align.md5 arc.scg.faa DB_BUILD_DATE img nr.md5 silva.nr_v132.tax arc.scg.lookup distributions keggdb.dmnd pfam silva.nr_v132.tax.md5 bac.all.faa eggnog.dmnd kegg.db.md5 Pfam-A.hmm taxon_marker_sets.tsv bacar_marker.hmm euk.hmm LCA_tax ReadMe test_data bac.hmm genome_tree marker.hmm selected_marker_sets.tsv (squeezeMeta) [zhanglj@admin db]$ pwd /mnt/hpc/home/zhanglj/squeezeMeta/SqueezeMeta/database/db

jtamames commented 5 months ago

Can you copy the SqueezeMeta_conf.pl file here?

Panda-smile commented 5 months ago

Can you copy the SqueezeMeta_conf.pl file here?

SqueezeMeta_conf.pl.txt

jtamames commented 5 months ago

Hum... weird. But your issue will probably be solved if you change last line of the SqueezeMeta_conf.pl file: $opt_db = "CazyDB"; by $opt_db = " /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/db.list" and run add_databases.pl again

Panda-smile commented 5 months ago

I'll try it now and feedback.

jtamames commented 5 months ago

I guess that at some point you ran add_database.pl with CazyDB as database name, and that changed SqueezeMeta_conf.pl

jtamames commented 5 months ago

Put the correct path for file db.list in SqueezeMeta_conf.pl

Panda-smile commented 5 months ago

Hello Professor, I am not sure if my db.list is correct? db.list.txt

A： CazyDB /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/cazy /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/CAZy_description.txt B： CazyDB /public/home/zhanglj/squeezemetatrans/Squeezemetacazy /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/CAZy_description.txt

I put the database and db.list location as follows： (squeezeMeta) [zhanglj@admin Squeezemetacazy]$ pwd /mnt/hpc/home/zhanglj/squeezemetatrans/Squeezemetacazy (squeezeMeta) [zhanglj@admin Squeezemetacazy]$ ls CAZy_description.txt cazy.dmnd db.list

  1. I modified SqueezeMeta_conf.pl $opt_db = "public/home/zhanglj/squeezemetatrans/Squeezemetacazy/db.list";

  2. run command：/public/home/zhanglj/miniconda3/envs/squeezeMeta/SqueezeMeta/utils/add_database.pl shotguntrans db.list （ nomatter A or B db.list it still erro as bellow）： Can't open EXTDB file db.list Functional assignment for COGS Found COG annotation file in /mnt/hpc/home/zhanglj/squeezemetatrans/shotguntrans/results/07.shotguntrans.fun3.cog, skipping KEGG Found KEGG annotation file in /mnt/hpc/home/zhanglj/squeezemetatrans/shotguntrans/results/07.shotguntrans.fun3.kegg, skipping Can't open EXTDB file public/home/zhanglj/squeezemetatrans/Squeezemetacazy/db.list PFAM Found COG annotation file in /mnt/hpc/home/zhanglj/squeezemetatrans/shotguntrans/results/07.shotguntrans.fun3.cog, skipping Calculating coverage for functions Can't open EXTDB file public/home/zhanglj/squeezemetatrans/Squeezemetacazy/db.list

jtamames commented 5 months ago

Because the path in SqueezeMeta_conf.pl is not well set. Please check it and type it correctly. I think it should be: $opt_db = "/public/home/zhanglj/squeezemetatrans/Squeezemetacazy/db.list.txt"; Also check if your file is named db.list or db.list.txt

Panda-smile commented 5 months ago

  1. modified db.list location as： $opt_db = "/public/home/zhanglj/squeezemetatrans/db.list";

  2. database lacation： (squeezeMeta) [zhanglj@admin Squeezemetacazy]$ ls CAZy_description.txt cazy.dmnd db.list： CazyDB /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/cazy /public/home/zhanglj/squeezemetatrans/Squeezemetacazy/CAZy_description.txt

  3. CazyDB(squeezeMeta) [zhanglj@admin squeezemetatrans]$ /public/home/zhanglj/miniconda3/envs/squeezeMeta/Meta/utils/add_database.pl shotguntrans db.list

Trends analyzed in the ”intermediate“ folder： Was it successful?

image
Panda-smile commented 5 months ago

@jtamames Hello Professor, it seems that this annotation is still unsuccessful. Can you please try again to find out what caused the problem?（resluts as below） , wish for your help!

  1. db.list.txt

  2. (squeezeMeta) [zhanglj@admin squeezemetatrans]$ cd Squeezemetacazy (squeezeMeta) [zhanglj@admin Squeezemetacazy]$ ls CAZy.Annotation cazy.dmnd (squeezeMeta) [zhanglj@admin Squeezemetacazy]$ pwd /public/home/zhanglj/squeezemetatrans/Squeezemetacazy

  3. run：time /public/home/zhanglj/miniconda3/envs/squeezeMeta/SqueezeMeta/utils/add_database.pl shotguntrans db.list

  4. main erro !!!!!!： Can't open fun3 CazyDB annotation file /mnt/hpc/home/zhanglj/squeezemetatrans/shotguntrans/results/08.shotguntrans.fun3.CazyDB

  5. erro details screenshot： image

  6. results is blank：

    image

files ：

image image
jtamames commented 5 months ago

The name of your file seems to be db.list.txt, not db.list

Panda-smile commented 5 months ago

SqueezeMeta_conf.pl.txt

The name of your file seems to be db.list.txt, not db.list

In order to upload the file I added the txt suffix

07.shotguntrans.fun3.CazyDB have generated. 08.shotguntrans.fun3.CazyDB was not generated in the results folder and I didn't find it either

image image image

image

jtamames commented 5 months ago

What happens if you run 07.fun3assign.pl shotguntrans?

Panda-smile commented 5 months ago

07.shotguntrans.fun3.CazyDB.txt

07.fun3assign.pl shotguntrans

07.shotguntrans.fun3.CazyDB已经生成。

image

jtamames commented 5 months ago

Ok. Then just do: cp 07.shotguntrans.fun3.CazyDB.txt 08.shotguntrans.fun3.CazyDB.txt in the results directory and try again

Panda-smile commented 5 months ago

好的。然后只需执行： cp 07.shotguntrans.fun3.CazyDB.txt 08.shotguntrans.fun3.CazyDB.txt 在结果目录中 并重试

Professor, it seems to be running, please wait for feedback. （wish successfuly）

image

Panda-smile commented 5 months ago

I am very grateful to the professor for helping me. I finally succeeded.

jtamames commented 5 months ago

Glad to hear. Closing issue

Panda-smile commented 5 months ago

很高兴听到。结题

  1. Hello Professor, I found that there are numerical numbers in the results. These do not correspond to any carbohydrate enzymes. I would like to ask if my annotation is reasonable?

image

  1. eg: (EC 2.4.1.183), in the yellow area in the picture, I only saw the corresponding EC number ((EC 2.4.1.183)) in the CAZy.Annotation file, but it was not shown in the table with annotations to GT5
  1. Profeesor，My understanding is that he gave the enzyme with the highest hit rate among the many options, so it was expressed as EC, right? image