Problem ccm

[qhelleu]

Hi,
I have a problem with the ccm module, I ran:

python ./GALA/ccm comparison_new 16

and got:
`

new_draft_121623
new_draft_135853
new_draft_101723
new_draft_112381
new_draft_164056
new_draft_145149
new_draft_153244
new_draft_82379
new_draft_95088
Traceback (most recent call last):
File "./GALA/ccm", line 35, in
scaffolding(path=paf,number_of_drafts=drafts,block=block,percentage=percent,shortage_contig=contig,quality=qty,out_file=True,output_name=name,output=output)
File "/scratch/GALA/src/scaffolding.py", line 211, in scaffolding
elif (d[base][n].split('\t')[-3].replace('\n','')==d[base][n+1].split('\t')[-3].replace('\n','')) and (d[base][n].split('\t')[5]==d[base][n+1].split('\t')[5]):
IndexError: list index out of range
`

Thanks,
Best.

[mawad89]

Hi;
I am working on it now, once I finish it I will let you know

Best

[qhelleu]

Hi,
I noticed that the problem occurs with some assemblies only. I can send them to you via PM if needed.

Thanks,
Best.

[mawad89]

Sorry for late response
You can try it now
If you get any other problems kindly pass it.
I am also added a new parameters for MDM to enhance it
Best wishes

[qhelleu]

Hi,
The problem has been solved, thanks.
But a new one raised!
At the very end of the ccm process I get the following error:

/usr/local/bin/gala/ccm comparison_new 16
new_draft_12 1623
new_draft_13 5853
new_draft_10 1723
new_draft_11 2381
new_draft_16 4056
new_draft_14 5149
new_draft_15 3244
new_draft_8 2379
new_draft_9 5088
new_draft_1 1028
new_draft_2 4085
new_draft_3 1285
new_draft_4 2335
new_draft_5 2144
new_draft_6 1180
new_draft_7 1414
Traceback (most recent call last):
File "/usr/local/bin/gala/ccm", line 35, in
scaffolding(path=paf,number_of_drafts=drafts,block=block,percentage=percent,shortage_contig=contig,quality=qty,out_file=True,output_name=name,output=output)
File "/usr/local/bin/gala/src/scaffolding.py", line 250, in scaffolding
zom=zom+int(a[ien][bac][0].split('\t')[1])
KeyError: 'ctg3181_awad'

Let me know if you need the assemblies.

Thanks,
Best.

[mawad89]

Hi;
If you can share your assemblies to see exactly why this problem appear

Thanks
Best

[mawad89]

Hi,
Just change the name of new_draft_1 to new_draft_01 and tell me if you face any other problem

Best

[injaci]

Hi,
I have a similar error with ccm with 2 draft assemblies.

New_draft_assemblies
new_draft_1.fa
new_draft_2.fa

comparison folder
(base) njacii@lyra04:~/ayb/gala>
-rw------- 1 njacii default 45804574 Aug 10 15:26 draft_1vsdraft_2.paf
-rw------- 1 njacii default 54549875 Aug 10 15:28 draft_2vsdraft_1.paf
-rw------- 1 njacii default 50417388 Aug 11 06:29 new_draft_1vsnew_draft_2.paf
-rw------- 1 njacii default 61314632 Aug 11 06:31 new_draft_2vsnew_draft_1.paf

njacii@lyra04:~/ayb/gala> ./ccm comparison 2
draft_1 19056
draft_2 30331
new_draft_1 19533
new_draft_2 30788
Traceback (most recent call last):
File "./ccm", line 35, in
scaffolding(path=paf,number_of_drafts=drafts,block=block,percentage=percent,shortage_contig=contig,quality=qty,out_file=True,output_name=name,output=output)
File "/home/njacii/ayb/gala/src/scaffolding.py", line 241, in scaffolding
for ya in scaffolds_list[ay].keys():
RuntimeError: dictionary changed size during iteration

[mawad89]

Hi,
I have a similar error with ccm with 2 draft assemblies.

New_draft_assemblies
new_draft_1.fa
new_draft_2.fa

comparison folder
(base) njacii@lyra04:~/ayb/gala>
-rw------- 1 njacii default 45804574 Aug 10 15:26 draft_1vsdraft_2.paf
-rw------- 1 njacii default 54549875 Aug 10 15:28 draft_2vsdraft_1.paf
-rw------- 1 njacii default 50417388 Aug 11 06:29 new_draft_1vsnew_draft_2.paf
-rw------- 1 njacii default 61314632 Aug 11 06:31 new_draft_2vsnew_draft_1.paf

njacii@lyra04:~/ayb/gala> ./ccm comparison 2
draft_1 19056
draft_2 30331
new_draft_1 19533
new_draft_2 30788
Traceback (most recent call last):
File "./ccm", line 35, in
scaffolding(path=paf,number_of_drafts=drafts,block=block,percentage=percent,shortage_contig=contig,quality=qty,out_file=True,output_name=name,output=output)
File "/home/njacii/ayb/gala/src/scaffolding.py", line 241, in scaffolding
for ya in scaffolds_list[ay].keys():
RuntimeError: dictionary changed size during iteration

Hi;
I think you are using Python3 you just need to change to Python2

[mawad89]

@injaci @qhelleu
Do you still have any problems?

[injaci]

Hi Awad, Yes, i after running ccm with python2 i got the following error. draft_2 30331 draft_1 19056 new_draft_2 30788 new_draft_1 19533 Traceback (most recent call last): File "./ccm", line 35, in <module> scaffolding(path=paf,number_of_drafts=drafts,block=block,percentage=percent,shortage_contig=contig,quality= qty,out_file=True,output_name=name,output=output) File "/home/njacii/ayb/gala/src/scaffolding.py", line 250, in scaffolding zom=zom+int(a[ien][bac][0].split('\t')[1]) KeyError: 'contig_23569_awad' Rgds Isaac

…

On Mon, Aug 24, 2020 at 6:24 PM Mohamed Awad ***@***.***> wrote: @injaci <https://github.com/injaci> @qhelleu <https://github.com/qhelleu> Do you still have any problems? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADCDKKGNUKBTPKHA6AQ6GDSCKAZFANCNFSM4OQPCKCA> .

-- *Isaac Njaci, PhD* Postdoctoral Scientist Department of Metabolic Biology John Innes Centre, Norwich Research Park Norwich, NR4 7UH, UK ------------------------------------------- Visiting Scientist Biosciences eastern and central Africa International Livestock Research Institute Box 30709, Nairobi 00100, KENYA Tel: +254 20 422 3805 | Mobile: +254 711 756905 Email: Isaac.Njaci@jic.ac.uk | Skype: injaci

[mawad89]

Hi Isaac
try the last commit

[qhelleu]

Works for me!
Thanks.
Best.