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Parsing input error #231
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I agree, the parsing errors should be more informative. I'll fix that. Could you tell me which version of |
I used |
Seems like that fixed it @ArtRand next time I'll review my input files instead of trusting the script! Sneaky updates sneak pass me... |
@Ge0rges I'm going to re-open this issue to track work for better error messages when input fails to parse. Some other users have encountered the same error and it's not clear enough what the problem is. |
Hi @ArtRand, I've also encountered a parsing error - I'm trying to run the script below, attempting to use the regions.bed.gz files as output from wf_human_variation --mod function. Have also tried with the wf_mods.bedmethyl.gz. For the -r /regions-bed, I download the NCBI refseq track in bed format. Define variables for pathsREF="/projects/health_sciences/oms/pathology/powry48p/202404ONT/reference/ref_genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna" Run modkit dmr./modkit dmr multi Error:
Any tips would be appreciated, thanks! |
Hello @Rpowellnz, Could you tell what $ head -n 5 refseq.bed looks like? |
Hi @ArtRand, The output from $ head -n 5 refseq.bed is as below, which I'm guessing is not correctly formatted.. Could you provide some guidance on how to generate the appropriate .bed file for -r/ for a genome-wide differential methylation analysis of protein coding genes? bplist00�_WebMainResource� _ebResourceTextEncodingName_WebResourceData_WebResourceMIMEType_WebResourceFrameName^WebResourceURLUUTF-8O�S<style type="text/css"></style> chr1 201283451 201332993 NM_000299 0 + 201283702 201328836 0 15 453,104,395,145,208,178,63,115,156,177,154,187,85,107,2920, 0,10490,29714,33101,34120,35166,36364,36815,38526,39561,40976,41489,42302,45310,46622, |
Hello @Rpowellnz, You certainly need to remove any of those HTML tags at the start. The BED file should be a plain text file with 3 or 4 tab-separated fields: |
Hi @ArtRand I removed the HTML tags so now $ head -n refseq1.bed produces the output below. chr1 201283451 201332993 NM_000299 0 + 201283702 201328836 0 15 453,104,395,145,208,178,63,115,156,177,154,187,85,107,2920, 0,10490,29714,33101,34120,35166,36364,36815,38526,39561,40976,41489,42302,45310,46622, Trying to run modkit dmr as below, still produces the error ./modkit dmr multi
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@Rpowellnz The latest version will report out which file is failing to parse. Could you confirm that it's an issue with the argument to |
Hi @ArtRand,
The following command which I believe to have executed on identical files in the past (perhaps on 0.3.0) seem to produce the error below now:
Error:
> Error! Parsing Error: Error { input: "\t\t", code: Many1 }
Is this due to a change/misformat in my input files that I might have missed or does it seem like a bug in modkit? The error is a buit mysterious.
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