import data

[TingTingShao]

Hi,

I have a problem with importing one specific fragment file, it shows errors:

snap.pp.import_data(
    "/data/sun/snap2/000fragments/D19-13001.fragments.tsv.gz",
    file="010h5ad/D19-13001.h5ad",
    chrom_sizes=snap.genome.hg38,
    min_num_fragments=1000,
    sorted_by_barcode=False,)

PanicException: called `Result::unwrap()` on an `Err` value: Custom { kind: Other, error: "MissingStartPosition: c" }

Could you please help me with this?

Thanks, tingting

[kaizhang]

Your file may be truncated. Check the last line of your file.

[TingTingShao]

Oh, it looks like the file is not complete, stops at chr9

(snap2) bash-4.4$ zcat sun/snap2/000fragments/D19-13001.fragments.tsv.gz | tail
chr9    113556607       113556656       TGCCTCAAGAGCTGTG-1      2
chr9    113556607       113556667       TGGCGCATCCATGTTT-1      1
chr9    113556623       113556671       GCCAGCACAAGGCTTT-1      1
chr9    113556634       113556669       CCGCATTAGGTGAACC-1      1
chr9    113556682       113556738       AACCTTTTCACTCGTC-1      1
chr9    113556711       113556870       TAGGAGGGTGTTGGTT-1      1
chr9    113556739       113556936       AAACTCGTCGGTTAGT-1      1
chr9    113556777       113556966       CCCGTTACATTACACG-1      1
chr9    113556787       113556822       ACAAAGAGTAAACGAT-1      1

So in this case, the file can not be processed in SnapATAC2?

[TingTingShao]

Hi,

I redownloaded the files, all 295 files were processed surprisingly fast for about 20 mins for basic QC.

Thanks! tingting

[TingTingShao]

solved