KeyError for extended_circular_fasta.write(header2joined_seq[contig2extended_status[contig]] + '\n') about cobra HOT 15 CLOSED

Hey LinXing,

Yeah, that seems to have fixed the issue! Both sample now run to completion 😄

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No problem and thank you for the rapid fix!

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Hi,

Thank you for your interest in COBRA, I am glad it helps for your analyses.

Regarding these two samples, could you please share these files with me , (1) COBRA_end_joining_pairs.txt (2) COBRA_potential_joining_paths.txt and (3) debug file?

Thank you.

Best,
LINXING

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Sure, here are those 3 files for sample 1 (key error in this case was 'NODE_67_length_39995_cov_222.169830')

COBRA_end_joining_pairs.txt
COBRA_potential_joining_paths.txt
debug.txt

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And here they are for sample 2 (key error here was 'NODE_404_length_6556_cov_28.183972')

COBRA_end_joining_pairs.txt
COBRA_potential_joining_paths.txt
debug.txt

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Thank you Chris. I will take a look ASAP and let you know what is the wrong.

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And here they are for sample 2 (key error here was 'NODE_404_length_6556_cov_28.183972')

COBRA_end_joining_pairs.txt COBRA_potential_joining_paths.txt debug.txt

Hi Chirs, unfortunately I was not able to locate the bug with the files you provided. Do you mind sharing all the input files of this sample, so I can run COBRA on my end and try to debug it? No worries if you do not want to do so.

LINXING

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Yeah sure no problem, I'll send them onto the gmail address you provided in a different issue post. Thanks again for taking a look at the issue!

In case you need it here is the command i'm running for sample 1 (so same for sample 2 except paths to files)

cobra-meta -f data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds.fasta -q data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds_over_2.5kb.fasta -
c data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds.coverage.formatted.txt -m data/processed/assemblies/spades_CTRLM08LongB03Faeces/scaffolds_sorted.bam -a metaspa
des -mink 21 -maxk 55 -t 10 -o data/processed/assemblies/spades_CTRLM08LongB03Faeces/cobra/ 

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Sent :)

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Sent :)

Hi Chris, unfortunately I do not see the email. Could you please confirm?

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I sent it to the linkingchanATgmailDOTcom address you posted in another issue. Is this not the correct email?

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i sent it via wetransfer so may be in your spam if that is the correct email

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I have checked and did not see it anywhere. My email address is [email protected]. Could you please share using googledoc or dropbox?

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Hi Chris, I think I was able to fix the bug. Could you please try this version and let me know if it works for you or not? Thank you.
cobra_test.py.zip

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That's good to know. Thank you for help. I will release a new version asap.

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