hickit.js error

[shiyi-pan]

Hi, I want to use this tool to find TADs but met a problem. here is my scripts:

first, I used minimap2 to mapping HiC reads to my genome:

$MINIMAP/minimap2 -ax sr NN1138-2.v1.0.genome.fasta soybean_R1.fastq.gz soybean_R2.fastq.gz > alignment.sam

then I try to Extracting contact pairs :

$HICKIT/hickit.js sam2seg alignment.sam | $HICKIT/hickit.js chronly - | gzip > contacts.seg.gz

but met an error:

: No such file or directory
: No such file or directory

I used the ls command to make sure the the path of hickit.js and alignment.sam is correct.
I tried to download the k8-linux from https://github.com/lh3/varcmp and put it into The environment variable But it didn't work.
Could you help me fix the problem. Thank you very much.

[tanlongzhi]

Hi, can you send me some of your data (e.g. a small SAM file), so that I can check if it works on my computer?

And yes, you do need k8 to use this repo. You can download k8 from its own repo.

Best,
Tan

[shiyi-pan]

thank you for your reply. I downloaded the k8 and it worked in my computer.
but I met another error when I run the following command:

$HICKIT/hickit -i contacts.seg.gz -o - | bgzip > contacts.pairs.gz

it told me that there was no sex chromosomes (identified by 'X' or 'Y' in chr names). here is the error log:

[W::hk_sd_ploidy_XY] no sex chromosomes (identified by 'X' or 'Y' in chr names)
[M::hk_pair_dedup] duplicate rate: -inf% = -1 / 0

My study species is soybean . there is no sex chromosomes in soybean . could you help me fix this problem , thank you again.

[tanlongzhi]

Sorry that this repo currently doesn't support a lack of sex chromosomes. I'll fix it and let you know as soon as I do.

Best,
Tan

[shiyi-pan]

ok , Thank you for your reply.