YAML Error: Expected separator '---' #40

[zwj426]

Dear @starskyzheng, I encountered a problem while using panpop, which was caused by an error in YAML/Loader. pm, resulting in the inability to correctly recognize parameters. May I ask if there is any way to solve it? Thanks!

perl $path/PART_run.pl -i 06.merge_samples.chr4.vcf -o ./test -r Ref.fa -t 2 --force --tmpdir ./tmp YAML Error: Expected separator '---' Code: YAML_PARSE_ERR_NO_SEPARATOR Line: 1 Document: 2 at ~/lib/YAML/Loader.pm line 88.

[starskyzheng]

Did you changed config files?

[zwj426]

Thank you for your reply. I didn't make any changes. I downloaded through ‘git clone https://github.com/StarSkyZheng/panpop.git’ and encountered the same error in both window and shell.

[starskyzheng]

Did you install PanPop using conda?

[zwj426]

I have tried to install it using conda, but unfortunately, I cannot find any tools related to PanPop in the virtual environment, such as 'PART_run.pl'.

conda env create -f conda.panpop.yaml conda activate panpop conda install -c bioconda svim-asm cpanm MCE::Channel Tie::CharArray

[starskyzheng]

You should run Part_run.pl which downloaded from https://github.com/StarSkyZheng/panpop.git in our conda env.

[zwj426]

Thanks again for your reply. I resolved the issues above and then successfully ran the case. However, when running my own data, I ran into some problems that others have had before, but I have absolutely no idea how to fix it, can you give me some advice. Here is my input file which merged SVs via bcftools concat merge. I would appreciate your [help!]

Duplicate specification "e|ext_bp_min=i" for option "e" Now reading ref fasta : Done reading ref fasta read 1958 contig / total 2770686120 bp Warn! aln software(muscle) exit status(2)! redo! No. 1 Warn! aln software(muscle) exit status(2)! redo! No. 1 Warn! aln software(muscle) exit status(2)! redo! No. 1 Warn! aln software(muscle) exit status(2)! redo! No. 1 Uploading data2.zip…

[starskyzheng]

Does the final result OK?

[zwj426]

Data2. zip is the SVs of chr27 after merging multiple SV callers and individuals, as well as the reference genome of chr27 in cattle. It is part of my results due to size limitations in file uploads.

[starskyzheng]

The file data2.zip failed to upload. So, Does the final result OK?

[zwj426]

No, it doesn't output any results. I re-uploaded the file, please try again. data2.zip

[starskyzheng]

Same a this issue ( https://github.com/starskyzheng/panpop/issues/18#issuecomment-1959763266 )

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