search

DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
250 stars 73 forks source link

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

Open nadiaandreani1 opened 6 years ago

nadiaandreani1 commented 6 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 6 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 6 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.

[TEF Gold]http://www.lincoln.ac.uk/opendays

The University of Lincoln, located in the heart of the city of Lincoln, has established an international reputation based on high student satisfaction, excellent graduate employment and world-class research.

The information in this e-mail and any attachments may be confidential. If you have received this email in error please notify the sender immediately and remove it from your system. Do not disclose the contents to another person or take copies.

Email is not secure and may contain viruses. The University of Lincoln makes every effort to ensure email is sent without viruses, but cannot guarantee this and recommends recipients take appropriate precautions.

The University may monitor email traffic data and content in accordance with its policies and English law. Further information can be found at: http://www.lincoln.ac.uk/legal.

mourisl commented 6 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 6 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 6 years ago

@MRuinels You need 106Gb of RAM.

MRuinels commented 6 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 4 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).