Error with Lastz mapping

Question: Error with Lastz mapping

2.8 years ago by

Brazil

Guilherme Dias • 110 wrote:

Hello mates,

I've been hiting upon this error over the last days (bellow)... I frequently use the Lastz tool and have even used it with this very same dataset a while ago. Is there something wrong with the server?

python: can't open file '/galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz/lastz_wrapper.py': [Errno 2] No such file or directory
/scratch/03166/xcgalaxy/main/staging/11939160/command.sh: line 40: /galaxy-repl/main/deps/samtools/0.1.18/env.sh: No such file or directory

lastz software error • 864 views

ADD COMMENT • link •

modified 2.7 years ago by kara.powder • 0 • written 2.8 years ago by Guilherme Dias • 110

2.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Our team is working to get Lastz functional on the public Main instance at http://usegalaxy.org. For details and progress, follow here:

https://github.com/jennaj/support-known-issues/wiki

https://github.com/galaxyproject/galaxy/issues/1622

Thanks for reporting the issue, Jen, Galaxy team

ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

2.7 years ago by

kara.powder • 0

United States

kara.powder • 0 wrote:

Hi Jen,

It looks like the issue was closed today, but I just ran Lastz and sam still getting the same error that I have bene getting for a few days now:

python: can't open file '/galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz/lastz_wrapper.py': [Errno 2] No such file or directory /scratch/03166/xcgalaxy/main/staging/12077424/command.sh: line 40: /galaxy-repl/main

ADD COMMENT • link written 2.7 years ago by kara.powder • 0

Hi Kara, I am running another test now to see if I can reproduce your error. The tool was fine earlier yesterday. We appreciate your feedback. I'll reply again after the test completes. Jen

ADD REPLY • link written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

All tests went quickly - Lastz is functional on all clusters at http://usegalaxy.org using a locally cached reference genome (I used hg19) or a custom reference genome.

Would you mind running your test again now? If there is another problem, you can send in a bug report. Please include a link to this biostars post in the comments.

Thanks, Jen

ADD REPLY • link written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen. It looks like it's working again. I'll do the bug report if i have further problems.

ADD REPLY • link written 2.7 years ago by kara.powder • 0

Please log in to add an answer.

Similar posts • Search »