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Maggi-Chen / Inspector

A tool for evaluating long-read de novo assembly results
MIT License
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Inspector error #16

Open mergi-2674 opened 1 year ago

mergi-2674 commented 1 year ago

Hi Maggi,

I have been using Inspector to check the assembled genome through Flye. However, continuously it gives me the same error even if I changed some default parameters. Here is the error, How it should be fixed? thanks

/home/xxxxx/Inspector/inspector.py -c genome.fasta -r genome.fastq.gz -d nanopore -t 20 . . . . . . Collect info from scaffold_96561_np12_RagTag_polished Collect info from scaffold_97192_np12_RagTag_polished Collect info from scaffold_97806_np12_RagTag_polished Collect info from scaffold_97933_np12_RagTag_polished Collect info from scaffold_98921_np12_RagTag_polished sh: 1: cat: Argument list too long sh: 1: cat: Argument list too long sh: 1: cat: Argument list too long Traceback (most recent call last): File "/home/xxxxxxx/Inspector/inspector.py", line 131, in cov=denovo_static.mapping_info_ctg(denovo_args.outpath,chromosomes_large,chromosomes_small,totalcontiglen,totalcontiglen_large) File "/home/xxxxxx/Inspector/denovo_static.py", line 138, in mapping_info_ctg splrate=round(10000*float(splitread)/mapped)/100.0 ZeroDivisionError: float division by zero

Best, Mergi

Maggi-Chen commented 1 year ago

Hello Mergi,

According to the error massage, it seems none of the reads are mapped to the contigs. Could you check the output directory and see if 'valid_contig.fa' contains contigs? If so, could you check if read_to_contig.bam contains read alignments with flag of 0 or 16?

Thanks, Maggi

RickyW94 commented 5 months ago

Hi, I'm getting the exact same issue. 'valid_contig.fa' contains contigs and 'read_to_contig.bam' contains read alignments with flags of 0, 16, 2048, 2064, etc. I'm curious to know if this was resolved and how.

fka21 commented 2 months ago

Hello, I'd also like to confirm this issue. As @Maggi-Chen asked I have checked that the valid_contigs.fa does in fact have entries and as @RickyW94 mentioned there are flags of different values present in the read_to_contig.bam (0, 16, 2048, 2046, 272, etc.). Has there been any progress on this error?

RickyW94 commented 2 months ago

@fka21 I gave up as there has been no response.