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wyan999
@wyan999
Hi, I used usegalaxy.org to run limma-voom. The datasets used are from the galaxy limma test data with the count files as Mut1.count, Mut2.count, Mut3.count and WT1.count, WT2.count, and WT3.count. Anno.txt was used as annotation and contrast as "Mut-WT". limma-voom failed with the error message as "Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
Calls: rownames<- ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
In addition: Warning message:
non-unique values when setting 'row.names':
Execution halte
3 replies
I installed limma-voom in our local galaxy. It gave the same error message as in usegalaxy.org. The limma-voom works well if use "Single Count Matrix" as the input. Meanwhile, there is no duplicate row names in the input files (Mut1, Mut2.. count files).
Niti Jadeja
@nitijadeja_twitter
Hello all,
I am new to Galaxy and was trying to analyse RNASeq data from the rabbit model. One of the steps in the tutorial mentions 'Annotatemyids' and it works in the case of the datasets from mice. Is there an alternative to Annotatemyid for genomes uploaded by users? For some reason, the Deseq does not accept my 'feature counts' file. When I tried Stringtie, converting the stringtie IDs to Gene id was an issue. Please guide.
RealYHD
@RealYHD
Hi, I'm also a new Galaxy user and recently, I've been getting Could not lookup the current user's information: user: unknown userid 819800 errors on BowTie2 and FASTQC, tools I've used before with no problem. If anyone could help I'd really appreciate it. I'd be happy to provide more logs and info on inquiry.
gcbryan89
@gcbryan89
Hi, I am getting errors using FastQC and Fastp. The error is "FATAL:  Couldn't determine user account information: user: unknown userid 819800". Can anyone help?
SabaterL
@SabaterL
Hi, I am having issues connecting to Galaxy. The error says: "Galaxy could not be reached" but there is not info on the status page. Any idea?
Marius
@mvdbeek:matrix.org
[m]
usegalaxy.org is being updated, it is listed in blue, under maintainance
SabaterL
@SabaterL
My bad, didn't see it! Cheers!
elbeckett2
@elbeckett2
Hi there, I just started Galaxy and have a basic online account. I am trying to run the alignment in the published paper by Minevech et al. 2012 that details the power of CloudMap in galaxy for comparing various c. elegans mutant strains to the hawaiian reference strain. According to the paper, everything should be done on the cloud. However, it seems that I need to download galaxy onto my computer to run it? I watched the video and know how to get the workflow and the published data to run it. However, whenever I try to run it I get this error:
" Workflow cannot be executed. Please resolve the following issue:
Following tools missing: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0, gatk_realigner_target_creator, gatk_indel_realigner, toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0, gatk_depth_of_coverage, gatk_unified_genotyper, gatk_variant_select"

So I went and downloaded mercurial and went to download the two tools from ToolShed. But I get another error:
"Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable third-party cookies in your browser."
I then read that I need to get an admin account or make my account upgrade to admin and I am assuming that requires me to download galaxy to my computer?
7 replies
sjthursby
@sjthursby
Hi, I just tried to log in to my account and it says "no such user or invalid password" and then when I try to reset the password, it says "Failed to produce password reset token, user not found" - Is there anything I can do to fix this?
Nate Coraor
@natefoo:matrix.org
[m]
@sjthursby: can you try logging in again, and if it still fails, send an email to galaxy-bugs@galaxyproject.org with the email address you are registered with (assuming you are using usegalaxy.org).
sjthursby
@sjthursby
Thank you
anthonyL
@anthonyLieures
Hi, I saw it was possible to use Docker as tool dependency resolvers. By default this feature uses the DockerHub registry but is it possible to pull containers from a private registry? And if so, is it possible to configure it from the Ansible deployment playbook?
RoberthAnthonyRojasChavez
@RoberthAnthonyRojasChavez
Hi, I am having some issues with Trim galore in the usegalaxy.org. I have it as part of a pipeline I built using Galaxy Version 0.6.7.
The issue is that upon completion it returns an empty file. I am re-running it on previous datasets where it finished with no issues, but it also returns empty datasets on those. Any help would be appreciated.
Running it using the [testing/development] galaxy cluster compute resource seems to allow trim galore to function normally
dheeraj-04
@dheeraj-04

Hi,

I’m using “sort data in ascending or descending order” tool on a locally installed galaxy server, to sort my data.

Whenever I use sort tool, the display shows “This job is currently running” and the job never gets completed.

All the tools work fine on local server, except for sort tool. Installed tool dependencies as well.

Is there any way to fix this? Any help is highly appreciated.

1 reply
Deepti
@Deepti66531796_twitter
Hi
Hi
I am having trouble logging into my account.
Can I please ask you is this an error on behalf of server?
I have been using usegalaxy.org to analyse my results. It took me a while to set up steps to perform my analyses. In fact the server has some data which I have now deleted from my computer. Can I please request you to restore my account as soon as possible as I am in the middle of my interpretation and analyses.
mmotoc
@mmotoc
Hello, I have been attempting to upload a large file (82 gb), and it was nearing completion (>80gb completed) but now it is saying the file is only at about 950 MB. What happened? I waited more than 15 hours for this upload to complete, is it starting over?
Marius
@mvdbeek:matrix.org
[m]
Most likely there was an error transmitting a fragment of the dataset, so Galaxy resumed from the first known chunk that was completed successfully, sorry about that.
If you have a way to refer to a remote URL you can let Galaxy fetch that dataset directly by pasting the URL in the upload dialog
mmotoc
@mmotoc
The job completed but I got a bus error. Any recommendations?
Marius
@mvdbeek:matrix.org
[m]
Can you send a bug report using the bug icon ?
RoberthAnthonyRojasChavez
@RoberthAnthonyRojasChavez
Hi, is galaxy main down? The status pages seems to say it is all ok.
2 replies
Damla Aygün
@aygun09_gitlab
Hi, I cannot run bcftools and freebayes tools.
Damla Aygün
@aygun09_gitlab
I'm trying to get vcf file, I've already get bam file with using bwa-mem, but freebayes is not run. It says "This is a new dataset and not all of its data are available yet.". Why?
1 reply
ireneiz
@ireneiz

Hi, last week I tried to log in in galaxy.org but I got this message: "This account has been marked deleted, contact your local Galaxy administrator to restore the account."
This is absolutely weird because I have only single account that I use for bioinformatic analysis; I worked on the platform last week and all was fine. I really don't understand why my account has been marked deleted.
Does anyone have the same problem?

I have already contacted the galaxy-bugs but no response has been done up to date.

snaik82
@snaik82
@simonbray:matrix.org Hi, the Gromacs simulation tool does not seem to be available on the US server.
4 replies
Nick Stoler
@nsto:matrix.org
[m]
FYI, stats.galaxyproject.eu has been down since at least yesterday
In case it hadn't been noted yet
It provides the job stats graph in the usegalaxy.eu middle pane
Dr Tiffany Kosch 👩‍🔬 🤿🐸🧬
@TAKosch_twitter
Hello, can someone tell me how I can see the run time for a job in Galaxy? I had a look at the "details" panel, but this only includes information about when the file was created
IrelCM
@IrelCM
Hello, I would like to report a little problem with Galaxy. When I select data from the Browser of multiple datasets it is not possible to click on samples using keys such as "shift" or "ctrl", so it is just possible select samples one by one and when there are more than 100 samples in the 2nd page after select one sample it changes to the first page again. If it is possible to you bring a hand, please...
bgruening
@bgruening:matrix.org
[m]
@IrelCM: thanks for the report very appreciated. Do you want to create a GitHub issue about that? We can show you how to do so.
2 replies
bgruening
@bgruening:matrix.org
[m]
@IrelCM: you need a Github account and then you can crate an issue here: https://github.com/galaxyproject/galaxy/issues
click on the green "New issue" button
Thanks!
jtt48
@jtt48

Trying to run a MicroRunQC but keep getting

An error occurred with this dataset:
[Errno 28] No space left on device: '/data/job_working_directory_s3/001/681/1681092/configs

Any idea of how to fix this?

bgruening
@bgruening:matrix.org
[m]
which server are you using?
mmotoc
@mmotoc
Hello, is anyone else having trouble with fastq uploads / RNASeq tools on the eu servers?
1 reply
mmotoc
@mmotoc
I uploaded some big files of rnaseq data (~80 gb each) and there are some lines in the data that appear to be giving the RNASeq tools some trouble in decoding. I can’t tell if this is just an error in the raw data, an instance of upload failure on the part of galaxy, or if the tools themselves are having troubles. If nobody else is having trouble with galaxy uploads nor the tools, I’ll assume the raw data is flawed, but do let me know if anyone notices any issues with uploads/RNASeq tools
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
mmotoc
@mmotoc

Hello, thank you. I ran the validation and got this output:
ERROR: Error in file /data/dnb06/galaxy_db/files/4/c/d/dataset_4cd2757c-eea1-4a57-a25b-bcda09e43b9e.dat: line 59026436: sequence and quality don't have the same length 125!=89

What does this mean, and how can I tell what file that is referring to?

kilibj
@kilibj
Hi, I am trying to recreate a macrogen whole exome sequencing pipeline in galaxy. Has anyone done this? what did you use instead of the GATK tools. Any help would be greatly appreciated.
ivywtl
@ivywtl
Hi, i have trouble accessing to galaxy (us server) throughout the day - the page just wouldn't load but it was working fine yesterday. Is there a problem with the server?
Marius
@mvdbeek:matrix.org
[m]
Yes, one of the servers is down, we're waiting on our infrastructure provider to give us an update.
mmotoc
@mmotoc
Hello, my fastq has some instances where quality and sequence are not the same length. What do you recommend I do? Is there a tool on galaxy to remove such instances?
bgruening
@bgruening:matrix.org
[m]
@mmotoc: this should not happen, please talk to your sequence facility. Maybe you data is really corrupted. I would trust it.