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MrOlm / inStrain

Bioinformatics program inStrain
MIT License
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inStrain plot not generating plots 2 and 7 #156

Closed cusoiv closed 11 months ago

cusoiv commented 1 year ago

Hi @MrOlm,

I seem to have run into a problem with inStrain plot. I wanted to generate a set of plots from the .IS object that I had previously created (which included also all the raw data, etc), but had problems with generating plots 2 and 7. This does not happen if I don't skip the plot generation in the inStrain profile -- then I get figures 2 and 7 just fine.

making plots 1, 2, 3, 4, 5, 6, 7, 8, 9 Plotting plot 1 Plotting plot 2 Failed to make plot #2: 'scaffold' Plotting plot 3 Plotting plot 4 Skipping plot 5 - you don't have all required information. You need to run inStrain genome_wide first Plotting plot 6 Plotting plot 7 Failed to make plot #7: 'scaffold' Skipping plot 8 - you don't have all required information. You need to run inStrain profile_genes first Plotting plot 9

It would be great if you could help in resolving this issue!

Thanks a lot, Annie

MrOlm commented 1 year ago

Hi @cusoiv -

Could you please run the command with -d (debug mode)? That will add some more output to explain what's going wrong. It would also be helpful to have the log file to try and troubleshoot this.

Best, Matt

cusoiv commented 11 months ago

Hi Matt,

Thanks for the instructions! I generated a log.log file with the inStrain plot ran in debug mode -- the parts for the inStrain plot should be at the end (the first half is the inStrain profile that I previously ran). I think the errors that showed up on the terminal were all written into the log file as well so I am not pasting them again here.

Thanks again! Annie log.log

MrOlm commented 11 months ago

OK thank you for this. One more question- in your raw_data folder there should be a file called raw_linkage_table.csv.gz. Could you please send that to me? That file is at the heart of this bug.

Best, Matt

cusoiv commented 11 months ago

Thank you Matt for the quick response! Please see the attachment for the relevant file.

Thanks again, Annie

On Wed, Jul 26, 2023 at 6:06 PM Matt Olm @.***> wrote:

OK thank you for this. One more question- in your raw_data folder there should be a file called raw_linkage_table.csv.gz. Could you please send that to me? That file is at the heart of this bug.

Best, Matt

— Reply to this email directly, view it on GitHub https://github.com/MrOlm/inStrain/issues/156#issuecomment-1652111545, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBFZZME4RGX2SLJT6EVOGLXSE56RANCNFSM6AAAAAA2B4WFBM . You are receiving this because you were mentioned.Message ID: @.***>

MrOlm commented 11 months ago

Hi Annie,

I don't believe attachments work in this way- you can either email me the file directly or upload it to GitHub (here https://github.com/MrOlm/inStrain/issues/156).

Thank you! MO

cusoiv commented 11 months ago

Hi Matt,

Thanks! Uploading now. raw_linkage_table.csv.gz

Best, Annie

MrOlm commented 11 months ago

OK- thank you for all of this. I have now confirmed that I understand the bug that's causing this issue, and I will fix it in the next inStrain update.

Thanks again! Matt

MrOlm commented 11 months ago

I believe this bug is fixed in version 1.7.6, released a few minutes ago

-MO

cusoiv commented 11 months ago

Thank you Matt! This is incredibly helpful!

On Wed, Jul 26, 2023 at 11:43 PM Matt Olm @.***> wrote:

Closed #156 https://github.com/MrOlm/inStrain/issues/156 as completed.

— Reply to this email directly, view it on GitHub https://github.com/MrOlm/inStrain/issues/156#event-9928965286, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBFZZJXGBJXN2SYDHH6I53XSGFRFANCNFSM6AAAAAA2B4WFBM . You are receiving this because you were mentioned.Message ID: @.***>