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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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Error! Parsing Error: Error { input: "m\t1", code: Digit } #209

Open saky7009 opened 1 week ago

saky7009 commented 1 week ago

(base) [mmolla@dg-gpunode06 ~]$ modkit dmr pair -a /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/duplex_pileup.bed.gz -b /gpfs2/scratch/mmolla/Longread_1/SP2/SP2_A/CPG_duplex_pileup.bed.gz -o /gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/cpg_islands_tumor_normal.bed -r /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/Withoutadjustmode/cpg_islands_ucsc_cleaned.bed --ref /gpfs2/scratch/mmolla/Z/HL4.fsa --base C --threads 4 --log /gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/dmr.log

reading reference FASTA at "/gpfs2/scratch/mmolla/Z/HL4.fsa" Error! Parsing Error: Error { input: "m\t1", code: Digit }

Why does it shown?

ArtRand commented 1 week ago

Hello @saky7009,

Could you show me the what $ head /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/Withoutadjustmode/cpg_islands_ucsc_cleaned.bed looks like and attach /gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/dmr.log?

Thanks.

saky7009 commented 1 week ago

/gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/dmr.log?

[src/logging.rs::52][2024-06-19 10:44:21][DEBUG] command line: modkit dmr pair -a /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/duplex_pileup.bed.gz -b /gpfs2/scratch/mmolla/Longread_1/SP2/SP2_A/CPG_duplex_pileup.bed.gz -o /gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/cpg_islands_tumor_normal.bed -r /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/Withoutadjustmode/cpg_islands_ucsc_cleaned.bed --ref /gpfs2/scratch/mmolla/Z/HL4.fsa --base C --threads 4 --log /gpfs2/scratch/mmolla/Longread_1/SP3A_control_SP2A_Tumor/dmr.log [src/dmr/tabix.rs::81][2024-06-19 10:44:21][DEBUG] looking for index associated with /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/duplex_pileup.bed.gz at /gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/duplex_pileup.bed.gz.tbi [src/dmr/tabix.rs::81][2024-06-19 10:44:21][DEBUG] looking for index associated with /gpfs2/scratch/mmolla/Longread_1/SP2/SP2_A/CPG_duplex_pileup.bed.gz at /gpfs2/scratch/mmolla/Longread_1/SP2/SP2_A/CPG_duplex_pileup.bed.gz.tbi [src/dmr/subcommands.rs::281][2024-06-19 10:44:21][INFO] reading reference FASTA at "/gpfs2/scratch/mmolla/Z/HL4.fsa" [src/bin/main.rs::22][2024-06-19 10:44:25][ERROR] Error! Parsing Error: Error { input: "m\t1", code: Digit }

ArtRand commented 1 week ago

@saky7009 could you send me the first few records from gpfs2/scratch/mmolla/Longread_1/SP3/SP3_B/Withoutadjustmode/cpg_islands_ucsc_cleaned.bed?