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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Cannot read .fa file #190

Closed NicMAlexandre closed 1 year ago

NicMAlexandre commented 1 year ago

Hello,

I have installed repeatmodeler using conda, and then tried again installing from source with multiple different versions. Everything seems to be fine during the installation step, including that of other software dependencies. Unfortunately, when running in the first round for about 45 minutes, I get a string of errors like this:

cannot read file .../RM_2830087.FriDec230816282022/round-1/family-125.fa cannot read file .../RM_2830087.FriDec230816282022/round-1/family-129.fa cannot read file .../RM_2830087.FriDec230816282022/round-1/family-103.fa

And then it progresses to round 2. Any help is greatly appreciated.

rmhubley commented 1 year ago

Thanks for reaching out to us. Unfortunately I would need much more information to understand what is going on in this case. What sort of machine are you running on? Is this a local or network filesystem? Do you have a copy of the screen log output from the very start of the run? I am surprised that the error message includes a path starting with "...". Can you give me the path of the directory you were in when you started the run and the full command line used?

BTW...This is the RepeatMasker github site. In the future I would recommend that issues like this be submitted to the RepeatModeler github at https://github.com/Dfam-consortium/RepeatModeler.

NicMAlexandre commented 1 year ago

Hi Robert,

I was able to determine that the installation worked correctly for RepeatModeler and the issue was that when running on a shared node, the process is inefficient. When I ran on a closed node with large memory, it worked fine. Thank you so much!

I will submit to that Github from now on.

On Thu, Jan 12, 2023 at 10:34 AM Robert Hubley @.***> wrote:

Thanks for reaching out to us. Unfortunately I would need much more information to understand what is going on in this case. What sort of machine are you running on? Is this a local or network filesystem? Do you have a copy of the screen log output from the very start of the run? I am surprised that the error message includes a path starting with "...". Can you give me the path of the directory you were in when you started the run and the full command line used?

BTW...This is the RepeatMasker github site. In the future I would recommend that issues like this be submitted to the RepeatModeler github at https://github.com/Dfam-consortium/RepeatModeler.

— Reply to this email directly, view it on GitHub https://github.com/rmhubley/RepeatMasker/issues/190#issuecomment-1380842535, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFB63375EFJB6FP3IEDE7O3WSBFBVANCNFSM6AAAAAATH5BNCU . You are receiving this because you authored the thread.Message ID: @.***>

-- Best,

Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley @. @.>