Several "At least one cluster failed!Stopping..." errors #261
Comments
|
Do you get a log.clusters file in the output folder? If so, what's been logged in it? |
|
I send attached all the files I get as output on the out.run folder, as
well as the original fastq.gz files.
When I use the --verbose flag I get the same error message, without any
additional information.
I'm using the ariba v. 2.11.1, which I installed using "sudo apt-get
install ariba" in Ubuntu 18.04.
25164_R1.fastq.gz
<https://drive.google.com/file/d/1uu-zgd2UhRNoUAQUeEBDTpx1KNm4LG95/view?usp=drive_web>
25164_R2.fastq.gz
<https://drive.google.com/file/d/1BFinhuu6iZC2-6T_NmAVwDYt3K1nLkCu/view?usp=drive_web>
Thank you for your help!
…On Thu, Mar 28, 2019 at 12:45 PM kpepper ***@***.***> wrote:
Do you get a log.clusters file in the output folder? If so, what's been
logged in it?
Also, do you get any extra information using the --verbose flag?
What version shows when you execute 'ariba version'
Are you able to provide access to the fastq files?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#261 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AIENl07pyk4WekMqVFRDT_fdz03Bk2yzks5vbKtXgaJpZM4cOb8z>
.
|
|
Hi @BaMagalhaes, The version of Ariba available in Debian is now rather out of date (the latest Ariba release is v2.13.15). I would suggest using the latest Ariba release via pip3 install or using the Docker hub image, which worked for me - see the Github page for instructions. |
|
I had indeed an older version of Ariba. Thus, I removed the package,
installed it again with pip3, ran it with the same command but the same errors
occurred:
'$ariba run --verbose out.card.prepareref' 25164_R1.fastq.gz
25164_R2.fastq.gz out.run
Found reads file: 25164_R1.fastq.gz
Found reads file: 25164_R2.fastq.gz
ARIBA version: 2.13.5
External dependencies:
bowtie2 2.3.4.1 /usr/bin/bowtie2
cdhit 4.7 /usr/bin/cd-hit-est
nucmer 3.1 /usr/bin/nucmer
External dependencies OK: True
Python version:
3.6.7 (default, Oct 22 2018, 11:32:17)
[GCC 8.2.0]
Python packages:
ariba 2.13.5
/home/localadmin/.local/lib/python3.6/site-packages/ariba/__init__.py
bs4 4.6.0 /usr/lib/python3/dist-packages/bs4/__init__.py
dendropy 4.3.0 /usr/lib/python3/dist-packages/dendropy/__init__.py
pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py
pymummer 0.10.3 /usr/lib/python3/dist-packages/pymummer/__init__.py
pysam 0.14 /usr/lib/python3/dist-packages/pysam/__init__.py
Python packages OK: True
Everything looks OK: True'
(...)
Error:
'Final value of remaining_clusters counter: Value('l', 81)
Stopping! Signal received: 13
Finished assembling clusters
Traceback (most recent call last):
File
"/home/localadmin/.local/lib/python3.6/site-packages/ariba/clusters.py",
line 612, in run
self._run()
File
"/home/localadmin/.local/lib/python3.6/site-packages/ariba/clusters.py",
line 646, in _run
raise Error('At least one cluster failed! Stopping...')
ariba.clusters.Error: At least one cluster failed! Stopping...
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/localadmin/.local/bin/ariba", line 310, in <module>
args.func(args)
File
"/home/localadmin/.local/lib/python3.6/site-packages/ariba/tasks/run.py",
line 65, in run
c.run()
File
"/home/localadmin/.local/lib/python3.6/site-packages/ariba/clusters.py",
line 615, in run
raise Error('Something went wrong during ariba run. Cannot continue.
Error was:\n' + str(err))
ariba.clusters.Error: Something went wrong during ariba run. Cannot
continue. Error was:
At least one cluster failed! Stopping...'
After this I removed the package again and tried to installed it with
docker but instead got another error (I believe not related to this
subject):
'$ docker pull sangerpathogens/ariba
Command 'docker' is available in '/snap/bin/docker'
The command could not be located because '/snap/bin' is not included in the
PATH environment variable.
docker: command not found'
I'm a bit stuck at the moment with this docker problem, but I'll try to
solve it and see if this installation is the solution for these errors.
…On Thu, Mar 28, 2019 at 6:11 PM kpepper ***@***.***> wrote:
Hi ***@***.*** <https://github.com/BaMagalhaes>*,
So, I ran your files on a Mac Ariba install and it produced a report.tsv
with no errors.
I ran an older Ariba release on Ubuntu 12 and got a Signal message but
still ran to completion and produced a report.tsv. It didn't abort.
I then ran your files through the latest Ariba release on Ubuntu 17 via
the docker image - again ran to completion with no errors.
The version of Ariba available in Debian is now rather out of date (the
latest Ariba release is v2.13.15). I would suggest using the latest Ariba
release via pip3 install or using the Docker hub image, which worked for me
- see the Github page for instructions.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#261 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AIENl8YQeQyOIIepnxN4bn2efnyJB6Fhks5vbPeygaJpZM4cOb8z>
.
|
|
Does it exit immediately, or do you get some output such as: AAC_3__Ib detected 1 threads available to it Is there anything at all in the out.run folder? To access Docker you could do the following: |
|
I did get something like that as output but there was nothing else, apart
from what I showed you previously, in the out.run folder.
Thank you for your help with docker. I manage to install Ariba after
exporting /snap/bin to PATH and adding my user to my docker group, since
I'm running the program as a non-root user.
I used the command :
$ docker run --rm -it -v home/ubuntu/data:/data sangerpathogens/ariba ariba
run --verbose out.card.prepareref 25164_R1.fastq.gz 25164_R2.fastq.gz
out.run
but I get the error:
docker: Error response from daemon: create home/ubuntu/data:
"home/ubuntu/data" includes invalid characters for a local volume name,
only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a
host directory, use absolute path.
See 'docker run --help'.
I just simply copied my files (25164_R1.fastq.gz, 25164_R2.fastq.gz,
out.card.prepareref) to home/ubuntu/data with sudo mv.
I'm sorry for the spamming with simple/obvious questions, but it's the
first time I run a program with docker.
…On Fri, Mar 29, 2019 at 11:02 AM kpepper ***@***.***> wrote:
Does it exit immediately, or do you get some output such as:
AAC_3__Ib detected 1 threads available to it
AAC_3__Ib reported completion
APH_3___IIb detected 1 threads available to it
APH_3___IIb reported completion
etc.
Is there anything at all in the out.run folder?
To access Docker you could do the following:
export PATH=/snap/bin/:$PATH
to add docker to your path before running the command. Do you have a
sysadmin who can check that it's installed properly?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#261 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AIENlw-7U05ZPygJvkSwv2nTMDSaoZ0Iks5vbeQCgaJpZM4cOb8z>
.
|
|
Are you missing a / in front of home/ubuntu... i.e. /home/ubuntu ? |
|
If I do:
$ docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/ariba
ariba run --verbose out.card.prepareref 25164_R1.fastq.gz 25164_R2.fastq.gz
out.run
The following reads file(s) were not found:
25164_R1.fastq.gz
25164_R2.fastq.gz
Cannot continue
But they are in /home/ubuntu/data:
localadmin@HOS46582:/home/ubuntu/data$ ls
25164_R1.fastq.gz 25164_R2.fastq.gz out.card.prepareref
…On Fri, Mar 29, 2019 at 2:43 PM kpepper ***@***.***> wrote:
Are you missing a / in front of home/ubuntu... i.e. /home/ubuntu ?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#261 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AIENl9UfScX1wJkc49OsZ88WEThILYNVks5vbhiYgaJpZM4cOb8z>
.
|
|
Yes, you need to put /data/ in front of the file args - it's the data area from the docker container's perspective: docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/ariba ariba run --verbose /data/out.card.prepareref /data/25164_R1.fastq.gz /data/25164_R2.fastq.gz /data/out.run |
|
Yap, it worked!
Thank you very much!
…On Fri, Mar 29, 2019 at 3:09 PM kpepper ***@***.***> wrote:
Yes, you need to put /data/ in front of the file args - it's the data area
from the docker container's perspective:
docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/ariba ariba
run --verbose /data/out.card.prepareref /data/25164_R1.fastq.gz
/data/25164_R2.fastq.gz /data/out.run
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#261 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AIENl-tqKGXrvmOHnb2KAY8Yev5OLtI6ks5vbh6ygaJpZM4cOb8z>
.
|
|
Great, good luck with your analysis. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
I tried to use ariba with the command:
$ ariba run out.card.prepareref 25164_R1.fastq.gz 25164_R2.fastq.gz out.runHowever I got the following errors
None of the solutions suggested in previous closed issues helped to solve these errors. I have tried it using the option
--threads 1, didn't help.Is it a bug? Do you have any other suggestions?
The text was updated successfully, but these errors were encountered: