Cannot generate output files with juicebox_assembly_converter.py

[mixiaoluo88]

Hi,
I tried to use the juicebox_assembly_converter.py script to generate the fasta file, but there seems to be something wrong in the assembly file to prevent this process.

The assembly file was generated from Juicerbox_1.11.08.

here is the command line:
python juicebox_assembly_converter.py -a new_assembly_file -f cx_geno.fasta

Processing assembly file. Details:
Assembly:                       new_assembly_file
Fasta:                         cx_geno.fasta
Output prefix:                  new_assembly_file
Contig mode:                    False
Simple Chromosome Names:        False

Reading sequences from cx_geno.fasta...
.
Sequences read

Reading .assembly file new_assembly_file...
.assembly read

Traceback (most recent call last):
  File "/home/20092008/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 872, in <module>
    processed_assembly = JuiceboxConverter().process(fasta, assembly,
  File "/home/20092008/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 91, in process
    sequences = self._add_breaks(sequences, assembly_map)
  File "/home/20092008/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 255, in _add_breaks
    assembly_map.sort(key=functools.cmp_to_key(cmp_assembly_map_entries))
  File "/home/20092008/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 331, in cmp_assembly_map_entries
    names1 = extract_contig_info(frag1[0])
  File "/home/20092008/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 368, in extract_contig_info
    names["index"] = int(frag_fiel
[cx_geno_hic.final.review.assembly.txt](https://github.com/phasegenomics/juicebox_scripts/files/7834628/cx_geno_hic.final.review.assembly.txt)
ds[-1].replace("fragment_", ""))
ValueError: invalid literal for int() with base 10: '122:prefix'

cx_geno_hic.final.review.assembly.txt

I have the similar error no matter how I try to run this script:

Checking for breaks listed in .assembly and making them...
Traceback (most recent call last):
  File "/home/yanyang_liang/Accessories/Softwares/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 875, in <module>
    simple_chr_names=simple_chr_names)
  File "/home/yanyang_liang/Accessories/Softwares/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 91, in process
    sequences = self._add_breaks(sequences, assembly_map)
  File "/home/yanyang_liang/Accessories/Softwares/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 271, in _add_breaks
    raise ContigNotFoundError('Could not find contig {0} in original FASTA'.format(fragment))
__main__.ContigNotFoundError: Could not find contig ('h1tg000001l:::fragment_1', '13505878') in original FASTA

[pengzhen688]

I met the same problem，I guess the script need some fix.
Traceback(most recent call last):
File "/ds3200_1/users_root/pengzhen/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 872, in processed_assembly = JuiceboxConverter().process(fasta, assembly,
File "/ds3200_1/users_root/pengzhen/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 91, in process sequences = self._add_breaks(sequences, assembly_map)
File "/ds3200_1/users_root/pengzhen/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py", line 300, in _add_breaks raise BadContigNameError("Unbroken contig {} failed to map!!".format(fragment_name))
main.BadContigNameError: Unbroken contig h2tg000001l failed to map!!

[mankiddyman]

@pengzhen688 Same error as you, I used hic-scaffolding-nf to generate my .hic and .assembly files successfully and then modified them in Juicebox also successfully. When I tried to convert the new final.assembly to .fasta I get the error:

[pengzhen688]

@pengzhen688 Same error as you, I used hic-scaffolding-nf to generate my .hic and .assembly files successfully and then modified them in Juicebox also successfully. When I tried to convert the new final.assembly to .fasta I get the error:

I just solve this problem, the fasta file with -f parameter should be the draft assemble file, as to me, it's the file after Hifiasm, it works but I still confused of the results are already chromosomal level, it couldn't name as chr but scaffold.
Attach my scripts and results.
/ds3200_1/users_root/pengzhen/software/juicebox_scripts/juicebox_scripts/juicebox_assembly_converter.py -a female.hap1.review.assembly -f female.hic.hap1.p_ctg.fa
part of my results sequence title:
PGA_scaffold_1__38_contigs__length_104764504 104764504
PGA_scaffold_2__1_contigs__length_85385853 85385853
PGA_scaffold_3__1_contigs__length_152023637 152023637
PGA_scaffold_4__1_contigs__length_3406 3406
PGA_scaffold_5__1_contigs__length_75600790 75600790
PGA_scaffold_6__2_contigs__length_111463799 111463799
PGA_scaffold_7__1_contigs__length_118074989 118074989
PGA_scaffold_8__1_contigs__length_111544484 111544484
PGA_scaffold_9__1_contigs__length_114164565 114164565
PGA_scaffold_10__3_contigs__length_551076 551076
PGA_scaffold_11__2_contigs__length_254286 254286
PGA_scaffold_12__10_contigs__length_95934091 95934091
PGA_scaffold_13__9_contigs__length_1739813 1739813
PGA_scaffold_14__1_contigs__length_86811578 86811578
PGA_scaffold_15__8_contigs__length_80280840 80280840
PGA_scaffold_16__1_contigs__length_889487 889487
PGA_scaffold_17__6_contigs__length_2478057 2478057
PGA_scaffold_18__5_contigs__length_1643997 1643997
PGA_scaffold_19__3_contigs__length_1392244 1392244
PGA_scaffold_20__2_contigs__length_553579 553579
PGA_scaffold_21__1_contigs__length_113850 113850
PGA_scaffold_22__1_contigs__length_11221 11221
PGA_scaffold_23__1_contigs__length_30543 30543
PGA_scaffold_24__1_contigs__length_59000 59000
PGA_scaffold_25__1_contigs__length_78129 78129
PGA_scaffold_26__1_contigs__length_154235 154235
PGA_scaffold_27__1_contigs__length_307851 307851
PGA_scaffold_28__1_contigs__length_999 999
PGA_scaffold_29__1_contigs__length_181554 181554
PGA_scaffold_30__1_contigs__length_31656 31656
PGA_scaffold_31__1_contigs__length_181036 181036