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Classifier for metagenomic sequences
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Could not locate a Centrifuge index corresponding to basename "..." Error: Encountered internal Centrifuge exception (#1) #144

Open nadiaandreani1 opened 5 years ago

nadiaandreani1 commented 5 years ago

Hi, it is very first time I use centrifuge. i have downloaded the indexes and put them in the centrifuge folder in a folder called "index". it contains 4 files .cf

here is the error I get

ubuntu@nadia-server:/media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta$ ./centrifuge -f -x /media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta/index/ /media/nadiadata/minion_Sarah/rawfiles/fasta/20180725_SK_cDNA.guppy1.4.3.fna Could not locate a Centrifuge index corresponding to basename "/media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta/index/" Error: Encountered internal Centrifuge exception (#1) Command: /media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta/centrifuge-class --wrapper basic-0 -f -x /media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta/index/ /media/nadiadata/minion_Sarah/rawfiles/fasta/20180725_SK_cDNA.guppy1.4.3.fna (ERR): centrifuge-class exited with value 1

can someone help me in solving this?

Nadia

mourisl commented 5 years ago

You need to provide the prefix of the index file name. For example, you have the index files xyz.{1,2,3,4}.cf, then in -x option, you should put /media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta/index/xyz .

Does this help?

nadiaandreani1 commented 5 years ago

Thanks a lot! yes, it helps and the analysis is actually starting. However my machine goes out of memory (64gb). I have already tried to split my file in 10 smaller files, but I keep having the same error.

Nadia

From: Li Song [mailto:notifications@github.com] Sent: 09 August 2018 19:56 To: infphilo/centrifuge centrifuge@noreply.github.com Cc: Nadia Andreani NAndreani@lincoln.ac.uk; Author author@noreply.github.com Subject: Re: [infphilo/centrifuge] Could not locate a Centrifuge index corresponding to basename "..." Error: Encountered internal Centrifuge exception (#1) (#144)

You need to provide the prefix of the index file name. For example, you have the index files xyz.{1,2,3,4}.cf, then in -x option, you should put /media/nadiadata/minion_Sarah/centrifuge-1.0.4-beta/index/xyz .

Does this help?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/infphilo/centrifuge/issues/144#issuecomment-411861053, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AeTRd72-3HtXTmB7duVjVPAIM-t_mhJ3ks5uPIXEgaJpZM4V2C4i.

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mourisl commented 5 years ago

The nt database requires about 105gb memory and its not splittable. You can either find a larger-memory machine or use other index.

MRuinels commented 5 years ago

Hello! I am encountering the same problem with the nt index. Do you need 106 Gb of RAM or 106 Gb of space on the harddisk? I have a 4 T hard disk and 64 Gb RAM and I can't run it :( However, with the p+h+v index it worked well. Thanks a lot

mourisl commented 5 years ago

@MRuinels You need 106Gb of RAM.

MRuinels commented 5 years ago

hi @mourisl! thanks for your reply!Indeed I was suspecting it was RAM...however....now I added the option --mm and at least it started!Now it's running since yesterday evening...hope to not find it crushed soon ;)

shashibioinfo commented 5 years ago

Hi @mourisl i have same issue while running centrifuge tool in mac even after providing the prefix of the index file name it shows error "Could not locate a Centrifuge index corresponding to basename "index/p_compressed+h+v."

i have used ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz files for index

if you can please help me in resolving this

thank you

GastonViarengo commented 3 years ago

The nt database requires about 105gb memory and its not splittable. You can either find a larger-memory machine or use other index.

Is this the memory requeriment also for the RefSeq database? I'm trying to make it work but been unsuccesful in creating a bacterial index (https://github.com/DaehwanKimLab/centrifuge/issues/199#issue-700590687).