The program failed to read in your coverage file

[Geize]

Hi Elaina,

Being simple, Bio.Alphabet was deleted from all the script and well as where written "IUPAC"..

But running again the Binsanity-wf , I got the message:

The program failed to read in your coverage file :(. Please check it to make sure it is in the right format.

The coverage files (binsanity.txt.cov and binsanity.txt.cov.x100.lognorm) were generated from previous BinSanity script.

I tried both files but no one works.

Any tips?

[edgraham]

Hello,

This is a perplexing issue that a couple of people have commented on but for some reason I can't seem to reproduce it and it doesn't seem to appear with any pattern or regularity. What has fixed it for most people has been re-setting the tab delimination. I uploaded a script to the github in utils 'makeFileTabDelimited.py https://github.com/edgraham/BinSanity/blob/master/utils/makeFileTabDelimited.py'. Pull this script down and run it as such:

$ python makeFileTabDelimited.py [Coverage File] > [Output FIle]

Then try running Binsanity again and see if it works. I am hoping the next big update that I am in the process of sanity checking for Binsanity2 will make this issue obsolete because with all likelihood it's a legacy module or function from python2 that didn't convert well to python3.

-Elaina

On Thu, Mar 25, 2021 at 2:15 AM Geize @.***> wrote:

Hi Elaina,

Being sample, Bio.Alphabet was deleted from all the script and well as where written "IUPAC"..

But running again the Binsanity-wf , I got the message:

The program failed to read in your coverage file :(. Please check it to make sure it is in the right format.

The coverage files (binsanity.txt.cov and binsanity.txt.cov.x100.lognorm) were generated from previous BinSanity script.

I tried both files but no one works.

Any tips?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/edgraham/BinSanity/issues/54, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEC7DIYEAZOYRAMXI5LZMV3TFL5MLANCNFSM4ZY6ILIA .

[addyblanch]

Hi @edgraham I'm having the same issue. This is fresh install (never used before) via conda. All dependancies are ok. The reformat script doesn't solve the issue.

For completeness I've checked Binsanity version through conda and it states 0.5.3 but doing Insanity --version it shows 0.5.2

Also using Binsanity-wf is the -f flag to the bam files? The readme says fasta

Thanks in advance Adam

[edgraham]

Hello Adam,

So I am about to push an update that hopefully will finally fix this issue with the coverage files. Unfortunately the tough thing has been that I haven't had the issue since i pushed version 0.4.4 so pinpointing the feature causing it has been difficult for me since I haven't been able to recreate it consistently. This latest version I am going to push changes the way I read in and close the coverage file and hopefully that will fix the issue. Look for version 0.5.4 later today.

In terms of the version that was on my end, I had updated the script but I forgot to change the config version so even though it was updated it was still saying it was the same version.

For Binsanity-wf you don't read in the bam files whatsoever. Binsanity-wf takes as input an assembly file and a coverage file produced by Binsanity-profile. So the wiki is correct that -f is for the fasta file.

-Elaina

On Tue, May 25, 2021 at 4:07 AM Adam Blanchard @.***> wrote:

Hi @edgraham https://github.com/edgraham I'm having the same issue. This is fresh install (never used before) via conda. All dependancies are ok. The reformat script doesn't solve the issue.

For completeness I've checked Binsanity version through conda and it states 0.5.3 but doing Insanity --version it shows 0.5.2

Also using Binsanity-wf is the -f flag to the bam files? The readme says fasta

Thanks in advance Adam

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/edgraham/BinSanity/issues/54#issuecomment-847775305, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEC7DI2YWDJC45YK4WNYVHDTPOAFNANCNFSM4ZY6ILIA .

[addyblanch]

Perfect thank you so much!! If I can help in anyway with providing log files of the error let me know :)

[edgraham]

Hello Adam,

If you have your log files its worth sending them along, maybe I'll be able to piece more together from them! But otherwise I did just update the pypi install and am working on the conda install which usually takes a little longer.

-Elaina

On Tue, May 25, 2021 at 9:30 AM Adam Blanchard @.***> wrote:

Perfect thank you so much!! If I can help in anyway with providing log files of the error let me know :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/edgraham/BinSanity/issues/54#issuecomment-848026344, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEC7DI65NMRGEKEQEKCS3ULTPPGA7ANCNFSM4ZY6ILIA .

[addyblanch]

Hi @edgraham just to report back, seems to be working fine after the update :)

[Chrisjrt]

Just wanted to post here in case anyone in the future gets the above error message and ends up at this post for the same reason I did.

For me, I got the above message as it turns out I misunderstood the wiki/help and was providing the path to the fasta in the -l parameter rather than just the name of the fasta file. i.e. the cause of the error actually had nothing to do with the coverage file itself... just human error :)