Question: Problems with HISAT2
gravatar for perrine.pegorier
2.6 years ago by
perrine.pegorier0 wrote:

When I use HISAT2, it fails with the error message: cannot find 'read_f'. I used it at the beginning of the week and it worked properly. I saw that it had been updated. Is the error due to this update?

software error • 1.3k views
ADD COMMENTlink written 2.6 years ago by perrine.pegorier0

Which version are you using?

ADD REPLYlink written 2.6 years ago by Bjoern Gruening5.1k

I am using it on the main Galaxy, Galaxy Version 1.0.1

ADD REPLYlink written 2.6 years ago by perrine.pegorier0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Galaxy main has been undergoing some major upgrades this week (as noted in the banner at However, I have not seen this particular error yet reported.

Two choices:

  1. Wait until the banner is removed, then re-run the job. If it fails, send in a bug report. I cannot give a firm time estimate for when this would occur right now.

  2. Send in a bug report now from the error dataset. Please make sure the inputs and error dataset are undeleted. Also try to limit the size of the history to just include the key datasets (copy these into a new history if needed as very large histories are difficult to review). Include a link to this Biostars post in the comments so that we can link the two. We can use your example to eliminate certain known issues, investigate and report new ones, use it for testing if/when a fix is needed, and to provide you with more feedback (generalized feedback we will post back here as an answer for others that may have run into the same issue). I didn't see a bug report already - but perhaps your Galaxy account and user name here at Biostars differ.

Thanks and I will watch for a bug report in case you decide to send one in. Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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