search

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
413 stars 181 forks source link

Calulate_map_resolution.sh issue #301

Open aminakur opened 1 year ago

aminakur commented 1 year ago

I am having an issue similar to #213 which wasn't resolved. I tried to use a nodups.pairs file generated with pairtools to run calculate_map_resolution.sh. I had the following output:

../opt/slurm/data/slurmd/job27576244/slurm_script: line 104: [: -lt: unary operator expected
./opt/slurm/data/slurmd/job27576244/slurm_script: line 153: [: -lt: unary operator expected
./opt/slurm/data/slurmd/job27576244/slurm_script: line 153: [: -lt: unary operator expected
./opt/slurm/data/slurmd/job27576244/slurm_script: line 153: [: -lt: unary operator expected
./opt/slurm/data/slurmd/job27576244/slurm_script: line 153: [: -lt: unary operator expected
./opt/slurm/data/slurmd/job27576244/slurm_script: line 153: [: -lt: unary operator expected

The map resolution is 100

The 50bp coverage file was empty. The input nodups.pairs file is analogous to merged_nodups.txt and contains the following fields: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type

I have previously used that file to generate .hic map with juicer pre successfully, so the file should not be corrupted.

Able-Andy commented 1 year ago

I've got the same problem with you, have you got it ?

aminakur commented 1 year ago

No

Able-Andy commented 1 year ago

What file is your input file? I uesd the HiC-Pro's *.allValidPairs.

aminakur commented 1 year ago

I used an output from pairtools. The input nodups.pairs file is analogous to merged_nodups.txt and contains the following fields: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type Can you please share what fields are in your file?

Able-Andy commented 1 year ago

I used the HiC-Pro's *.allValidPairs and contains the following fields: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag] Using this inputfile, I got the <50bp coverage file>, but have the same error as you.

Today, I use the file from juicer, it works.

aminakur commented 1 year ago

Can you please provide the column names in your file?

Able-Andy commented 1 year ago

You can get those in the file:

For more details :https://github.com/aidenlab/juicer/wiki/Pre#file-format