search

RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
88 stars 15 forks source link

[Seq_ID]_mtDNA_contig.png not created #63

Closed AkshitaJain2709 closed 1 week ago

AkshitaJain2709 commented 3 weeks ago

Hello,

The output from MitoFinder is giving all the files except [Seq_ID]_mtDNA_contig.png schematic representation of the annotation of the mtDNA contig. Could you please let me know how can I extract that file. Thanks

RemiAllio commented 3 weeks ago

Hi,

Thank you for your message.

Is there any "error" message in the geneChecker.log or geneChecker_error.log files? Also, are you using the last version of MitoFinder?

Overall, I recommend using the MitoFinder singularity image, with all dependencies already installed, to avoid potential MitoFinder's errors due installation issues.

Let me know if this helps! Best, Rémi

AkshitaJain2709 commented 3 weeks ago

Dear Remi

Thanks for your reply.

I am getting the following message:

Organism type specified: 1 alignCutOff: 30.0 coveCutOff: 7 Checking protein-coding genes, tRNAs and rRNAs from reference with organismType=1... Formatting database for blast... Formatting database for blast... rrnL rrnS Features found: 13 Total features: 14

Running tRNA annotation with mitfi Total features found after mitfi: 28

Could not import Image or ImageDraw library, no image of result being created. tRNA-Asp = 8497,8561 ND5 = 8281,9021

Should I install any dependency?

Thanks

RemiAllio commented 3 weeks ago

Yes you would need to install pillow.

Here is the way I do it during the singularity image creation:

wget  https://bootstrap.pypa.io/pip/2.7/get-pip.py  
python2.7 get-pip.py  
pip2.7 install pillow==6.2.2

Hope this helps! Best, Rémi

RemiAllio commented 1 week ago

Hi,

Does it work now?

Best, Rémi

AkshitaJain2709 commented 1 week ago

Dear Remi

It didn’t work, but I imported the gff file in Geneious prime for visualisation. Thanks for your help, really appreciate it.

Thanks, Akshita

Akshita Jain (she/her) | PhD Candidate | Plant Pathology

School of Applied Systems Biology | La Trobe University

AgriBio Centre | Agriculture Victoria Research | Department of Jobs Precincts and Regions

5, Ring Road, La Trobe University, Bundoora, VIC 3083

T: 9032 7129| M: 0452499270 | E: @.**@.>

[Image]

We work flexibly at Agriculture Victoria Research. I am sending this message now because this time suits me, and I encourage you to read, respond or action this email at a time that best works for you.

OFFICIAL

From: Rémi Allio @.> Sent: Wednesday, September 4, 2024 10:03:25 PM To: RemiAllio/MitoFinder @.> Cc: Akshita Jain (DEECA) @.>; Author @.> Subject: Re: [RemiAllio/MitoFinder] [Seq_ID]_mtDNA_contig.png not created (Issue #63)

EXTERNAL SENDER: Do not click links or open attachments unless you recognise the sender and know the content is safe.

Hi,

Does it work now?

Best, Rémi

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/RemiAllio/MitoFinder/issues/63*issuecomment-2328786378__;Iw!!C5rN6bSF!H9MSnbcK3J3VEpTVm3Ay1u7sFG34dFCUFmySHftwyctSmt-XqevnUsoKtrD2c_nVcRSUanlBlS8yBQvkLxOmJvubTpER1AGVMCaIRx0$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A2SQSPDQSMZ2TM4YGBN3GR3ZU3ZI3AVCNFSM6AAAAABNHGQDT6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRYG44DMMZXHA__;!!C5rN6bSF!H9MSnbcK3J3VEpTVm3Ay1u7sFG34dFCUFmySHftwyctSmt-XqevnUsoKtrD2c_nVcRSUanlBlS8yBQvkLxOmJvubTpER1AGVQiHIVNY$. You are receiving this because you authored the thread.Message ID: @.***>

RemiAllio commented 1 week ago

Oh, sorry for the inconvenience... IMO the best option would have been to use the singularity container to obtain the png from MitoFinder. But the geneious visualization tool is good so hopefully it works for you like that!

Best, Rémi