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js2264 / HiCool

Processing Hi-C raw data within R
https://js2264.github.io/OHCA/principles.html#hicool-hicstuff-within-r
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Error in Generating multi-resolution .mcool file #3

Closed AnakimG closed 2 weeks ago

AnakimG commented 4 months ago

Hi @js2264,

When running the HiCool function like that : x <- HiCool( r1 = './MKL30_Merged_R1.fastq.gz', r2 = './MKL30_Merged_R2.fastq.gz', restriction = 'HpaII', resolutions = c(500, 1000, 2000, 5000, 10000), genome = './genome_SL1344.fasta', output = './HiCool_MKL30_Merged/' )

I get this error : HiCool :: Generating multi-resolution .mcool file... Error in py_call_impl(callable, call_args$unnamed, call_args$named) : TypeError: 'int' object is not iterable Run reticulate::py_last_error() for details. Calls: HiCool ... -> force -> -> py_call_impl Execution halte

I feel like it is a fastq files problem, because on certain fastq files it works and on others it doesn't. Do you have any clue ? Thanks in advance

Anakim

js2264 commented 4 months ago

Hi @AnakimG, sorry I have no idea where this issue could originate from. The fastq files that work come from the same source that MKL30 reads? If two fastq files are corrupted and do not have identical # of reads, this could perhaps lead to such issue?