Placing bins in reference genome tree about checkm

[donovan-h-parks]

Hello Silas,

I think you may have caught CheckM in the middle of a version update. It looks to me like you have the latest CheckM code, but an outdated copy of the CheckM dependency data. Can you try running:

>checkm data update

This should identify the changed files and download them for you. Please let me know how you go.

Cheers,
Donovan

[S-vick]

Hi Donovan,

I ran ">checkm data update" and got the following output:

---

[CheckM - data] Check for database updates. [update]

---

Connecting to ACE server.

---

0 new file(s) to be downloaded from source
7 existing file(s) to be updated
123.43 MB will need to be downloaded
Confirm you want to download this data
Changes WILL be permanent
Continue? (y,n) : y

---

(re) creating manifest file (please be patient)

However, once this finished I tried to run ">checkm tree" and got the same errors as in my first post.

Regards,
Silas.

[donovan-h-parks]

Hey Salias,

I think I've isolated the issue. Please try updating the data again. Thank you for bringing this issue to my attention. This sort of issue is hard to debug locally.

Regards,
Donovan

[S-vick]

Hi Donovan,

Thanks for your speedy responses to my issues. I ran update data again and got the following output:

---

[CheckM - data] Check for database updates. [update]

---

Connecting to ACE server.

---

10 new file(s) to be downloaded from source
0 existing file(s) to be updated
58.22 MB will need to be downloaded
Confirm you want to download this data
Changes WILL be permanent
Continue? (y,n) : y

---

---

The following 6 file(s) are scheduled to be removed
genome_tree/genome_tree_prok.refpkg
genome_tree/genome_tree_prok.refpkg/phylo_modelytLSd6.json
genome_tree/genome_tree_prok.refpkg/genome_tree.final.tre
genome_tree/genome_tree_prok.refpkg/genome_tree.concatenated.derep.fasta
genome_tree/genome_tree_prok.refpkg/CONTENTS.json
genome_tree/genome_tree_prok.refpkg/genome_tree.derep.log
Confirm you want to delete these files
Changes WILL be permanent
Delete files? (y,n) : y

---

/home/silas/checkdata/genome_tree/genome_tree_prok.refpkg/phylo_modelytLSd6.json

Unexpected error: <type 'exceptions.OSError'>
Traceback (most recent call last):
File "/usr/local/bin/checkm", line 710, in
checkmParser.parseOptions(args)
File "/usr/local/lib/python2.7/dist-packages/checkm/main.py", line 1179, in parseOptions
self.updateCheckM_DB(options)
File "/usr/local/lib/python2.7/dist-packages/checkm/main.py", line 83, in updateCheckM_DB
DBM.runAction(options.action)
File "/usr/local/lib/python2.7/dist-packages/checkm/checkmData.py", line 129, in runAction
self.update()
File "/usr/local/lib/python2.7/dist-packages/checkm/checkmData.py", line 167, in update
prompt=True)
File "/usr/local/lib/python2.7/dist-packages/screamingbackpack/manifestManager.py", line 282, in updateManifest
os.remove(delete)
OSError: [Errno 2] No such file or directory: '/home/silas/checkdata/genome_tree/genome_tree_prok.refpkg/phylo_modelytLSd6.json'

Regards,
Silas.

[donovan-h-parks]

Hey Silas,

Obviously all this requires a bit of a rethink on my part.

To get you moving forward, can you try deleting everything in your CheckM
data directory (including all folders) EXCEPT the .dmanifest file. Then
trying running the data update again. If that doesn`t work, you can
manually grab the data files at
https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_20112014.tar.gz.
Extract the contents to a fresh folder and point CheckM to this folder with
checkm data setRoot .

Hopefully one of these solutions will work! :)

Cheers,
Donovan

On Mon, Dec 1, 2014 at 7:28 PM, S-vick [email protected] wrote:

Hi Donovan,

Thanks for your speedy responses to my issues. I ran update data again
and got the following output:

---

[CheckM - data] Check for database updates. [update]

---

Connecting to ACE server.

---

10 new file(s) to be downloaded from source
0 existing file(s) to be updated
58.22 MB will need to be downloaded
Confirm you want to download this data
Changes WILL be permanent
Continue? (y,n) : y

---

---

The following 6 file(s) are scheduled to be removed
genome_tree/genome_tree_prok.refpkg
genome_tree/genome_tree_prok.refpkg/phylo_modelytLSd6.json
genome_tree/genome_tree_prok.refpkg/genome_tree.final.tre
genome_tree/genome_tree_prok.refpkg/genome_tree.concatenated.derep.fasta
genome_tree/genome_tree_prok.refpkg/CONTENTS.json
genome_tree/genome_tree_prok.refpkg/genome_tree.derep.log
Confirm you want to delete these files
Changes WILL be permanent
Delete files? (y,n) : y

---

/home/silas/checkdata/genome_tree/genome_tree_prok.refpkg/phylo_modelytLSd6.json

Unexpected error:
Traceback (most recent call last):
File "/usr/local/bin/checkm", line 710, in
checkmParser.parseOptions(args)
File "/usr/local/lib/python2.7/dist-packages/checkm/main.py", line 1179,
in parseOptions
self.updateCheckM_DB(options)
File "/usr/local/lib/python2.7/dist-packages/checkm/main.py", line 83, in
updateCheckM_DB
DBM.runAction(options.action)
File "/usr/local/lib/python2.7/dist-packages/checkm/checkmData.py", line
129, in runAction
self.update()
File "/usr/local/lib/python2.7/dist-packages/checkm/checkmData.py", line
167, in update
prompt=True)
File
"/usr/local/lib/python2.7/dist-packages/screamingbackpack/manifestManager.py",
line 282, in updateManifest
os.remove(delete)
OSError: [Errno 2] No such file or directory:
'/home/silas/checkdata/genome_tree/genome_tree_prok.refpkg/phylo_modelytLSd6.json'

Regards,
Silas.

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[S-vick]

Hi Donovan,

I deleted all files (bar the .dmanifest file) and tried the data update command but this only added the genome_tree directory (and files within). So I manually downloaded the files you linked me to, extracted the contents, redirected checkm to the new directory with "checkm data setRoot" and ran "checkm tree" again which ran with no errors this time.

Thanks for sorting that out for me.

Regards,
Silas.