snp_index must be size 0 or 1, not 2 [pileup_and_phase.R]
#47
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Hi, did you check if the pileup counts and phased vcfs are not empty? |
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In the pashed folder there's nothing, the script is not generating any file.
```
x21922_mm8/
├── [ 0] phasing
├── [206K] pileup
│ └── [206K] x21922_mm8
│ ├── [ 60] cellSNP.base.vcf
│ ├── [206K] cellSNP.samples.tsv
│ ├── [ 60] cellSNP.tag.AD.mtx
│ ├── [ 60] cellSNP.tag.DP.mtx
│ └── [ 60] cellSNP.tag.OTH.mtx
└── [ 369] run_pileup.sh
```
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Are you sure this is a human hg38 bam? Most times this happens when the bam genome version does not match the SNP site VCF. |
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Totally sure. Data was generated with |
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What is the format of your barcodes? Should be 1 barcode per line. Do they match the barcodes in your bam? I would test with barcode list output by 10x under Since this is clearly an issue with the pileup, you could test with the command running |
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Hi @teng-gao , I am getting the same error while running run_numbat() on a single sample from a single individual. run_numbat() worked fine on 4 samples so far. pileup_and_phase ran without errors on this sample, and the pileup and phasing vcfs are not empty. This error occurs just after the "Building phylogeny" step. Do you have suggestions on things to check? Thank you! |
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Hi @laijen000 , I'm not sure which error you're referring to - did you mean to raise this issue on another related thread? Best, |
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Hi Teng,
Sorry, I mean the snp_index issue reported in this thread/subject line! The
error message is the same as reported here.
…On Mon, Jan 9, 2023 at 8:10 AM Teng Gao ***@***.***> wrote:
Hi @laijen000 <https://github.com/laijen000> ,
I'm not sure which error you're referring to - do you mean to raise this
issue on another related thread?
Best,
Teng
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In |
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Just a Question - has this error been fixed? This is still open and we also run into this error. |
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Here is our current error message: |
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Oh and that is how we got ran the analysis: |
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Hi @stela2502, I'm still not convinced that this is a bug rather than problem with input.. the error message says:
This cannot be right with 10x data. What's the format of your |
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Thank you for the fast reply. I came to know that this sample is not a cancer sample. And the problems cause is likely also that the previous step did not identify any SNPS. So it might be of help if you could actually capture this error and replace it by something more meaningful like "Sorry, but there are no SNPS I could analyze in your set -> exiting". This would actually get you rid of this 'issue'. So please be kind to us inexperienced ones and produce a better error message than this! |
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About the file format - I'll check, but would expect it to be correct. |
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Hmm, please let me know what specifically you see in your output folder. Does the pileup folder indeed contain empty files? A normal sample is totally ok and should help with germline SNP genotyping. |
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Really strange. My co-worker has still not checked the cell ids. Which exact version of the cell-ids do you need? the ones with /-1$/ or the ones without? |
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Hi teng-gao. Thank you for asking again and - yes the file format was of cause wrong. Would be cool to have a more informative error message - especially without all the python error before. What is the point of running the whole first step if you only get one line of data and that line of data even contains some clearly not cell_id specific items like ,; or \t. That are two checks that could easily be included into the first program - or? So why spend a lot of time on processing a bam file when the likelihood of a result == 0. |
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Ok, leaving a note here for better error handling and input format checking |
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I am the colleague of Stela2502 thank you for the advice it ran as expected. The error message was: But these files were not produced by the numbar run. What did we do wrong? The output from a Thank you for your help! |
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@coldhart88 I think you only ran the preprocessing step and not Numbat workflow itself. Also please open separate issues for different errors. Thanks |
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Hi, I'm running the first step (
pileup_and_phase.R)...... and having the following error:
What could I been missing, please?
(I'm running the docker container from singularity)
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