No valid pairs found problem

[sshen82]

Hi, I was using two hic matrices (generated from juicer with -k KR and resolution only 1000000, chromosome only chr1) and trying to use chess sim but shows the following error. Do you know the possible reason? By the way, what is shown is the same if @1000000@KR are eliminated.

2021-02-03 14:11:52,877 INFO Running '/p/keles/schic/volumeC/SiqiShen/miniconda3/envs/chess/bin/chess sim /p/keles/schic/volumeA/Script/Downstream/higashi/higashi_H1Esc_chr1_estimated.bed.hic@1000000@KR /p/keles/schic/volumeA/Script/Downstream/higashi/higashi_HAP1_chr1_estimated.bed.hic@1000000@KR /p/keles/schic/volumeA/Script/chess/chr1.bed /p/keles/schic/volumeA/Script/chess/higashi_H1Esc_HAP1_chr1_results.tsv --oe-input'
2021-02-03 14:11:53,828 INFO CHESS version: 0.3.6
2021-02-03 14:11:53,828 INFO FAN-C version: 0.9.14
2021-02-03 14:11:53,831 INFO Loading reference contact data
2021-02-03 14:12:04,050 INFO Loading query contact data
2021-02-03 14:12:14,455 INFO Loading region pairs
2021-02-03 14:12:14,455 WARNING 15 region pairs have been dropped, because they involve chromosomes that are not present in the provided contact data.
2021-02-03 14:12:14,455 ERROR No valid region pairs found; aborting.

[sshen82]

chess pairs hg19 100000000 10000000 /p/keles/schic/volumeA/Script/chess/chr${i}.bed --chromosome chr${i}
This is the code to generate the bed file.

chess sim /p/keles/schic/volumeA/Script/Downstream/higashi/higashi_${C1[$index]}_chr${i}estimated.bed.hic@1000000@KR /p/keles/schic/volumeA/Script/Downstream/higashi/higashi${C2[$index]}chr${i}estimated.bed.hic@1000000@KR /p/keles/schic/volumeA/Script/chess/chr${i}.bed /p/keles/schic/volumeA/Script/chess/higashi${C1[$index]}${C2[$index]}_chr${i}_results.tsv --oe-input
And this is the code to run sim.

[kaukrise]

Hi, Juicer removes the chr prefix from chromosomes during matrix generation. Have you tried to remove the chr prefix in the BEDPE file? Maybe that fixes the issue.

[sshen82]

It works! There is another problem showing up "Could not compute similarity for 10 region pairs. This can be due to faulty coordinates, too smallregion sizes or too many unmappable bins" then.

[nickmachnik]

If no other errors occurred, you should have gotten a valid output file, is that right?
The program just prints this info to indicate that not all of the regions defined in the input bedpe could be compared.

[sshen82]

Yes, it worked. Thanks for your help!