cooccurrence_matrices/absolute lists wrong SNP

[ibseq]

Hi DIllon,
I noticed in the cooccurrence_matrices/absolute path that one of the variants has a SNP that is not listed in the mutations.tsv file: specifically , the location is correct but the nucleotide change is wrong: how is this possible and how can I troubleshoot it? I checked many times and re-run it many times. I'm assuming is listed wrong in al other output files.

the snp in question is at position 23012: it has different nctl changes depending on variant. could this be the issue? checked the other variant outputs and they have even different snps in their files, not what I stated in the mutation file.

thanks
ibseq

[dorbarker]

Thanks for the bug report. I will look into it.

Could you provide a copy of the mutations file and the cooccurence matrix? You should be able to attach it here, or paste them into gist.github.com

[ibseq]

Hi Dillon
any update? - Sent you the two files privately

thanks
ibseq

[dorbarker]

Apologies - I was on vacation. I'm back to work on mmmvi now.

However, I don't see any files in my email nor linked anywhere on github.

[ibseq]

Hi Dillon Apologies and hope you had a nice rest. If I remove one of the variants, it runs fine…not sure why. Here’s the mail I sent time ago: I’ve since then run it many times by simply not including one variant ….

…

Begin forwarded message: From: "irene z.b." ***@***.***> Subject: Re: [dorbarker/voc-identify] cooccurrence_matrices/absolute lists wrong SNP (#41) Date: 14 July 2021 at 19:59:07 BST To: Author ***@***.***> Hi Dillon See attached. This is just one samples out of many - they all have same issue. I only looked at 23102 but not sure if other positions have been affected. Can you please not publish the data in the attached file? Thanks BW Irene On 28 Jul 2021, at 15:57, Dillon Barker ***@***.***> wrote: Apologies - I was on vacation. I'm back to work on mmmvi now. However, I don't see any files in my email nor linked anywhere on github. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH76DQYGPOLQ6SXZBP3AAS3T2ALGPANCNFSM5ALMW6VQ>.

[dorbarker]

Hmm. Weirdly enough, I don't see it - not even accidentally diverted to spam. Sorry about that. Could I trouble you to send it again?

[ibseq]

Hi Dillon Will you be able to help with the error below? Snakelike worked only on s bunch of bam file within folder. Tried to run the single samples and got this: - (mmmvi) ***@***.***:~/MMMVI/LIV_SAMPLES$ mmmvi --bam bams/7601_2107902_09_S31.mapped.primertrimmed.sorted.bam --reference data/reference.fasta --mutations data/mutations.tsv --outdir reports/7601_2107902_09_S31.mapped.primertrimmed.sorted/ --only-vocs BBB 2021-09-10 13:33:18 Begin 2021-09-10 13:33:18 Loading reads from bams/7601_2107902_09_S31.mapped.primertrimmed.sorted.bam 2021-09-10 13:33:40 Searching for reference signature mutations 2021-09-10 13:41:23 Searching for BBB signature mutations 2021-09-10 13:49:25 Formatting and writing reports 2021-09-10 13:49:25 Formatting summary Traceback (most recent call last): File "/pub28/ibseq/miniconda2/envs/mmmvi/bin/mmmvi", line 10, in <module> sys.exit(main()) File "/pub28/ibseq/miniconda2/envs/mmmvi/lib/python3.8/site-packages/mmmvi/mmmvi.py", line 121, in main reporting.write_reports(mutation_results, vocs, reads, args.outdir, args.delimiter) File "/pub28/ibseq/miniconda2/envs/mmmvi/lib/python3.8/site-packages/mmmvi/lib/reporting.py", line 541, in write_reports write_summary(voc_results, vocs, reads, outdir, delimiter) File "/pub28/ibseq/miniconda2/envs/mmmvi/lib/python3.8/site-packages/mmmvi/lib/reporting.py", line 485, in write_summary summary = format_summary(voc_results, vocs, reads) File "/pub28/ibseq/miniconda2/envs/mmmvi/lib/python3.8/site-packages/mmmvi/lib/reporting.py", line 80, in format_summary max_coverage = theoretical_maximum(reads, vocs) File "/pub28/ibseq/miniconda2/envs/mmmvi/lib/python3.8/site-packages/mmmvi/lib/reporting.py", line 168, in theoretical_maximum position_ranges = sorted(vocs[voc].keys()) TypeError: '<' not supported between instances of 'int' and 'NoneType'

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On 28 Jul 2021, at 21:42, Dillon Barker ***@***.***> wrote: Hmm. Weirdly enough, I don't see it - not even accidentally diverted to spam. Sorry about that. Could I trouble you to send it again? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH76DQYBS72AEMGWGNMPI7TT2BTRRANCNFSM5ALMW6VQ>.

[dorbarker]

Hello ibseq,
I just fixed this yesterday. Updating to version 0.10.2 should do the trick. You can confirm your version with mmmvi --version