Megablast 454 dataset

Question: Megablast 454 dataset

3.0 years ago by

colum.connolly • 10

European Union

colum.connolly • 10 wrote:

Dear Galaxy,

I posted a question on Monday 30th November with regards processing

of a data set. Unfortunately I am still getting the message " job is waiting to run".

I uploaded the data set on Friday and today I noticed that in the " view details of job" icon that

the filesize is given as 0 bytes.

Is this normal?

Thank you for your help.

Cheers

Colum

galaxy • 769 views

ADD COMMENT • link •

modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by colum.connolly • 10

A few questions:

1) What is the size and type of the dataset (note compression format along with type - fastq is assumed).

2) How was upload performed? URL, browser upload from a desktop, FTP?

3) Where are you using Galaxy? Public Main server at http://usegalaxy.org or somewhere else? Your own local or cloud Galaxy? Or another public server (please share URL if so)? Or an internal Galaxy set up at your institution/company?

The prior answer (Megablast 454 data) was with respect to http://usegalaxy.org. If the problems are there, we can look at your account, but the specifics about the data format/upload method will help.

Thank you for the details! Jen, Galaxy team

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifer,

Thank you for replying to my query so swiftly. My dataset consists of 10 MIDS from a sequencing run on a GS junior. I demultiplexed using software on the GS Junior. The mids contain numerous contigs in FNA file format. The size of the files are quite small ranging from 5 kb to 40 kb. I followed the screencast workflow on the Galaxy website “Processing and analysis Of 454 data in metagenomic studies”. I uploaded my data from the desktop. I am using the public main server @ https: // usegalaxy.org. I hope this information helps you uncover the problem.

Kind regards

Colum

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: 02 December 2015 19:17 To: Connolly, Colum Subject: [galaxy-biostar] C: Megablast 454 dataset

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Comment: Megablast 454 dataset<http: biostar.usegalaxy.org="" p="" 15214="" #15219="">:

A few questions:

1) What is the size and type of the dataset (note compression format along with type - fastq is assumed).

2) How was upload performed? URL, browser upload from a desktop, FTP?

The prior answer (Megablast 454 data<https: biostar.usegalaxy.org="" p="" 15172=""/>) was with respect to http://usegalaxy.org. If the problems are there, we can look at your account, but the specifics about the data format/upload method will help.

Thank you for the details! Jen, Galaxy team

ADD REPLY • link written 3.0 years ago by colum.connolly • 10

3.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello!

Thanks for the additional information. The browser used could be a factor (this is a new issue discovered in the last few days). If using IE, please test one (or more) of these browsers as an alternative: Firefox, Chrome, and Safari, in order to see if that resolved the problem. This browser change worked for another user recently (they used Firefox).

Our team will be reviewing why IE has issues initiating upload jobs.

Please see the related question: upload file through ftp

If not using IE, but another web browser not in the set of three above, please give test them anyway. It would be great if you could let us know which web browser is in use originally. We want to help resolve the root problem and resolve it, for all cases.

Results about how the alternate browsers worked would be great feedback (success or failure). And if a failure, we can explore the issue in more detail.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifer,

I have tried Firefox and google Chrome this morning, however still No luck with the megablast. Would it be an issue with the firewall in my Institute?

Kind regards

Colum

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: 03 December 2015 16:56 To: Connolly, Colum Subject: [galaxy-biostar] A: Megablast 454 dataset

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Megablast 454 dataset<http: biostar.usegalaxy.org="" p="" 15214="" #15227="">:

Hello!

Our team will be reviewing why IE has issues initiating upload jobs.

Please see the related question: upload file through ftp<https: biostar.usegalaxy.org="" p="" 15153=""/>

Results about how the alternate browsers worked would be great feedback (success or failure). And if a failure, we can explore the issue in more detail.

Thanks! Jen, Galaxy team

ADD REPLY • link written 3.0 years ago by colum.connolly • 10

Hi Jennifer,

I tried the workflow using Firefox and Google chrome, however the i received The following error messages for all megablasts;

Traceback (most recent call last): File "/scratch/03166/xcgalaxy/main/staging//11086525/tool_files/megablast_wrapper.py", line 22, in <module> import os, subprocess, sys, tempfile ImportError: No module named subprocess Traceback (most recent call

I am not sure what this message means. Would it be possible for you to have a look at my account.

Cheers

Colum

From: Jennifer Hillman Jackson on Galaxy Biostar [mailto:notifications@biostars.org] Sent: 03 December 2015 16:56 To: Connolly, Colum Subject: [galaxy-biostar] A: Megablast 454 dataset

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: Megablast 454 dataset<http: biostar.usegalaxy.org="" p="" 15214="" #15227="">:

Hello!

Our team will be reviewing why IE has issues initiating upload jobs.

Please see the related question: upload file through ftp<https: biostar.usegalaxy.org="" p="" 15153=""/>

Results about how the alternate browsers worked would be great feedback (success or failure). And if a failure, we can explore the issue in more detail.

Thanks! Jen, Galaxy team

ADD REPLY • link written 3.0 years ago by colum.connolly • 10

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