low_confidence.bed empty file about craq HOT 6 OPEN

Thank you very much for your support. . It seems that the long-read data you provided (lr.fq.gz) did not exact. You supplied long-read data, but CRAQ appears to have only used short-read data;

Is your command was craq -g assembly.fa -sms lr.fq.gz -ngs SRR10382366_1.fastq, SRR10382366_2.fastq -x map-hifi ？

Please check if your 'lr.fq.gz' file exists. Additionally, If you are using symbolic links of "lr.fq.gz" , please ensure that the filename of lr.fq.gz is the same to your raw SMS.fq file.

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Additionally, may I ask if your lr.fq.gz file actually exists? If you only have short-reads data, you can use the following command: 'craq -g assembly.fa -ngs SRR10382366_1.fastq, SRR10382366_2.fastq'.

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Indeed my error! I might have just worked out our other issue too. I will report back.
Agnieszka

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Alright, Agnieszka. Additionally, I need to point out that if you want to verify errors in the genome, the two files "locER_out/out_final.CRE.bed " and "strER_out/out_final.CSE.bed" are more valuable, as they mainly impact the final AQI value and the out_final.Report results. The file "low_confidence.bed" only reports regions in the genome with relatively low reads coverage, and it might be empty. To avoid potential confusion for users , I am considering moving this file to another folder."

If you have trouble, let me know.

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Ok, thanks! Would it be possible to maybe also update the documentation with '"low_confidence.bed" only reports regions in the genome with relatively low reads coverage'? Current wording is a bit ambiguous and I think my students understood it wrong.

I think one other thing we might have run into is that some of our genomes have large chromosomes and need a csi index, but I don't think this is handled.

Agnieszka

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Hi, Agnieszka,
Thanks, the documentation was update to avoid potential confusion.

If you encounter the following issue :
“[E::hts_idx_check_range] Region 631441106..631444822 cannot be stored in a bai index. Try using a csi index
[E::sam_index] Read 'sms2' with ref_name='ref1', ref_length=998496443, flags=256, pos=631441107 cannot be indexed
samtools index: failed to create index for "LRout/tmp_bam/sms.fa_sort.bam": Numerical result out of range”

Don't worry, CRAQ will continue to run. In fact, I only use the .bai suffix to ensure that the BAM file is sorted.

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