hickit.js:457: Error

[chenggang108]

Hi

I run into the problem as following, Can you please help with it?

hickit.js:457: Error: [File] Fail to open the file
	file = new File(args[getopt.ind]);
        ^
Error: [File] Fail to open the file
    at hic_bedflt (hickit.js:457:9)
    at main (hickit.js:723:28)
    at hickit.js:730:1

Thanks

Gang

[tanlongzhi]

Hi Gang,

It seems the BED file you're using (for hickit.js bedflt) cannot be opened. Can you tell us the command you're using, and attach your input files?

Best,
Tan

[chenggang108]

Hi Tan,

Here is how I ran the program

`./k8 hickit.js sam2seg -v b6_cast_snp_chr_parentheses.tsv aln.sam.gz | ./k8 hickit.js chronly - | ./k8 hickit.js bedflt par.bed - | gzip > contacts.seg.gz

The sam and tsv files are too big to attach. Do I need to provide a bed file? I thought that's generated by the previous step.

Thank you very much,

Gang

`

[tanlongzhi]

Hi Gang,

This error is caused by missing the file par.bed during the step | ./k8 hickit.js bedflt par.bed -.

Depending on the purpose of your analysis, a BED file par.bed may be required. In particular, for haplotype imputation and 3D modeling of a single diploid male cell, this file must be supplied, so that contacts involving the PARs can be removed (because this repo does not support 3D modeling of PARs in male cells).

If that is not your purpose, you can simply delete the step | ./k8 hickit.js bedflt par.bed -.

Best,
Tan

[chenggang108]

Hi Tan.

Thank you so much. I am kind of new in the field of data analysis. Did nor realize the need for the bed file. I do no have the file in hand. Can you please kindly provide it?

Thanks

Gang

[tanlongzhi]

Hi Gang,

Here I've attached the BED files for the human hg19 genome and for the mouse mm10 genome, respectively. The files are quite simple, containing just the (0-based) genomic coordinates of each PAR.

hg19.par.bed.gz
mm10.par.bed.gz

Best,
Tan

[chenggang108]

Hi Tan,

Thank you so much,

Gang

[chenggang108]

I got the information when after running, Does it mean there is something wrong with my SNP file?

WARNING: a new allele A on read E00526:261:H773CCCX2:7:1101:11485:62980 at position chr4:37046608 (not C/T)
WARNING: a new allele C on read E00526:261:H773CCCX2:7:1101:13778:27187 at position chr7:87372925 (not G/A)
WARNING: a new allele C on read E00526:261:H773CCCX2:7:1101:13839:27222 at position chr7:87372925 (not G/A)
WARNING: a new allele T on read E00526:261:H773CCCX2:7:1101:17614:21948 at position chr9:33098399 (not A/G)
WARNING: a new allele T on read E00526:261:H773CCCX2:7:1101:18923:20454 at position chr10:84269456 (not G/C)
WARNING: a new allele A on read E00526:261:H773CCCX2:7:1101:18944:34518 at position chr9:73823632 (not T/C)
WARNING: conflicting phase at a segment of read E00526:261:H773CCCX2:7:1101:22617:60571
WARNING: a new allele T on read E00526:261:H773CCCX2:7:1101:31477:59991 at position chr10:35550755 (not C/G)
WARNING: a new allele A on read E00526:261:H773CCCX2:7:1101:31619:13580 at position chr4:22307624 (not C/G)
.
.
.
.

[tanlongzhi]

This is completely normal. I typically redirect these warning messages to a log file, so they don't flood your screen:

hickit -i contacts.seg.gz -o - 2> contacts.pairs.log | bgzip > contacts.pairs.gz

[chenggang108]

Thank you, Tan,

[chenggang108]

Can I skip the impute step?

[chenggang108]

It looks the program does not allow me to use the raw contact.pair file directly.

./hickit -i contacts.pairs.gz -Sr1m -c1 -r10m -c5 -o no_imput.flt.pairs
[M::hk_map_read] read 675992 pairs
[M::hk_pair_filter_close_legs] filtered out 0/675992 pairs with close legs
[M::hk_pair_dedup] duplicate rate: 0.00% = 0 / 675992
hickit: main.c:188: main: Assertion `(m->cols & 0x3c) == 0x3c' failed.
Aborted

[tanlongzhi]

Technically you can skip imputation; but you can only use contacts whose both legs are haplotype-resolved. In other words, for each (non-header) row of contacts.pairs.gz, the two columns phase0 and phase1 must be either 0 or 1, but never ..

Therefore, to skip imputation, you must first remove any contacts with . in either of the two phase columns. You may do so using for example awk.

[chenggang108]

Than you Tan,

I got my first reconstruction from my data.

Best

Gang

[tanlongzhi]

Hi, I can't find the comment from your latest email, but you need to use the latest version of this repo to have the #unit line in the output .3dg file.

[chenggang108]

Hi Tan,

Sorry that I delete the previous issue. Because I found that my .3dg does not have #unit line. I am regenerating the file. But it looks the new file does not have the line either. Everything looks fine except the #unit line. What may cause this?