[BUG] chromap map Hi-C short reads Parameters: error threshold

[Hanjiangna]

I ran the chromap tool with Hi-C preset parameters on my data, and while the output SAM file (R0301onthap2.sam) was successfully generated, there was a message displayed that listed several mapping parameters:

Plaintext Parameters: error threshold: 4, min-num-seeds: 2, max-seed-frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 1000, MAPQ-threshold: 1, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90 However, I am unsure if this constitutes an error or is just a status report of the used settings. Could you please clarify whether these parameter values indicate any issues in the processing? If it's indeed an error, what might be causing it, and how can I resolve it? code chromap --preset hic -r R0301HifiHicOnt.asm.hic.hap2.p_ctg.fa -x contigs.index --remove-pcr-duplicates -1 Rhc_1_clean.fastq.gz -2 Rhc_2_clean.fastq.gz --SAM -o R0301onthap2.sam -t 50

error Parameters: error threshold: 4, min-num-seeds: 2, max-seed-frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 1000, MAPQ-threshold: 1, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90

[mourisl]

This is not an error. They are for the log.

[Hanjiangna]

Thanks for the prompt response!