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vmaffei / dada2_to_picrust

Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)
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Problem with vsearch #18

Closed marlenec closed 5 years ago

marlenec commented 5 years ago

Hi,

I am trying the tutorial you provided to get metagenome PICRUST estimations from DADA2 output. First part of the tutorial works fine, and I successfully intalled vsearch on my mac. However when I am typing in R : system('vsearch --usearch_global genome_prediction/gg_13_5_study_db.fasta.pre --db genome_prediction/97_otus.fasta --matched genome_prediction/gg_13_5_study_db.fasta --id 0.97')

I get the following error : vsearch v2.8.4_macos_x86_64, 16.0GB RAM, 8 cores https://github.com/torognes/vsearch Fatal error: Unable to open matched output file for writing

I guess there is a problem with the file gg_13_5_study_db.fasta, which indeed does not exist because we didn't create it in previous steps of the tutorial. Or maybe I missed something ?

Thank you,

Marlene

vmaffei commented 5 years ago

Hi Marlene, are you still having trouble with vsearch? When you get a chance, run sudo chmod a+w vsearch This will give your vsearch binary write permissions. Retry the vsearch step afterwards. If you still have trouble, feel free to post back!

marlenec commented 5 years ago

Hi, thank you so much for your answer ! I tried : system('sudo chmod a+w vsearch --usearch_global genome_prediction/gg_13_5_study_db.fasta.pre --db genome_prediction/97_otus.fasta --matched genome_prediction/gg_13_5_study_db.fasta.pre --id 0.97') But got this error :

sudo: no tty present and no askpass program specified

So, after reading this subject on an ubuntu forum (https://askubuntu.com/questions/281742/sudo-no-tty-present-and-no-askpass-program-specified), I tried this : system('sudo -S ./binary vsearch --usearch_global genome_prediction/gg_13_5_study_db.fasta.pre --db genome_prediction/97_otus.fasta --matched genome_prediction/gg_13_5_study_db.fasta.pre --id 0.97') R tried to run the command, but couldn't :

Password:Error: Unable to establish connection with R session Error: Unable to establish connection with R session

I am trying to start R with sudo from the beginning... Let's see.

vmaffei commented 5 years ago

Whoops, let me clarify my instructions!

Outside of R, in a terminal window, navigate to your copy of vsearch and then type sudo chmod a+w vsearch. This will give vsearch permission to write out data, if it already isn't allowed to do so. If no errors occur, reopen R and retry the vsearch step as written in the tutorial. No need to try anything like system('sudo chmod a+w vsearch... once back inside R.

Let me know how that goes for you!

marlenec commented 5 years ago

Hi, I just tried this, and it seems to work ! Thank you a lot !

vmaffei commented 5 years ago

No problem! Please feel free to post any question you might have in the future!