ValueError: line 496: object identifier out of order

[wuxingbo1986]

Dear all,

anyone have solution to the "ValueError: line 496: object identifier out of order" error ?

I looked at #21 and tries to change the parameter but still have the error.

I am scaffolding the contigs from ccs using an reference genome. Here is the code I used:

ragtag.py scaffold -C -g 100 -m 100 -f 10000 primary_final.fasta m54334U_All4cells.ccs.asm.bp.p_ctg.fa --mm2-params '-x asm20' -o ragtag_ccs -t 40

Thank you.

[malonge]

Hi there,

Can you please share the output logged to stderr?

Thanks, Mike

[wuxingbo1986]

here it is:

Tue Jul 20 15:55:02 2021 --- RagTag v1.0.1 Tue Jul 20 15:55:02 2021 --- CMD: /software/7/apps/ragtag/1.0.1/bin/ragtag_scaffold.py -C -g 100 -m 100 -f 10000 primary_final.fasta m54334U_All4cells.ccs.asm.bp.p_ctg.fa --mm2-params -x asm20 -o ragtag_ccs -t 40 Tue Jul 20 15:55:02 2021 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'. Tue Jul 20 15:55:02 2021 --- Mapping the query genome to the reference genome Tue Jul 20 15:55:02 2021 --- Running: minimap2 -x asm20 primary_final.fasta m54334U_All4cells.ccs.asm.bp.p_ctg.fa > ragtag_ccs/query_against_ref.paf 2> ragtag_ccs/query_against_ref.paf.log Tue Jul 20 22:33:38 2021 --- Finished running : minimap2 -x asm20 primary_final.fasta m54334U_All4cells.ccs.asm.bp.p_ctg.fa > ragtag_ccs/query_against_ref.paf 2> ragtag_ccs/query_against_ref.paf.log Tue Jul 20 22:33:38 2021 --- Reading whole genome alignments Tue Jul 20 22:33:42 2021 --- Filtering and merging alignments Tue Jul 20 22:33:48 2021 --- Ordering and orienting query sequences Tue Jul 20 22:33:48 2021 --- Writing scaffolds Tue Jul 20 22:33:48 2021 --- Writing: ragtag_ccs/ragtag.scaffolds.agp Traceback (most recent call last): File "/software/7/apps/ragtag/1.0.1/bin/ragtag_scaffold.py", line 528, in main() File "/software/7/apps/ragtag/1.0.1/bin/ragtag_scaffold.py", line 506, in main write_orderings(output_path + "ragtag.scaffolds.agp", output_path + "ragtag.confidence.txt", query_file, mapped_ref_seqs, fltrd_ctg_alns, pad_sizes, gap_types, make_chr0, overwrite_files, not remove_suffix) File "/software/7/apps/ragtag/1.0.1/bin/ragtag_scaffold.py", line 154, in write_orderings agp.add_seq_line(*out_agp_line) File "/software/7/apps/ragtag/1.0.1/lib/python3.7/site-packages/ragtag_utilities/AGPFile.py", line 170, in add_seq_line self._raise_line_err(line_number, "object identifier out of order") File "/software/7/apps/ragtag/1.0.1/lib/python3.7/site-packages/ragtag_utilities/AGPFile.py", line 71, in _raise_line_err raise ValueError(message)

Thanks.

[malonge]

Hi there,

Would you be able to update to v2.0.1? If so, rerun using the latest code and let me know how it goes, again sharing the stderr if there is a problem.

Anything >v2 is backwards incompatible, so you will need to start from scratch (delete the previous output directory).

[wuxingbo1986]

installed with conda and tried but still the error, see below;

Traceback (most recent call last): File "/home/xingbo.wu/.conda/envs/ragtag/bin/ragtag_scaffold.py", line 577, in main() File "/home/xingbo.wu/.conda/envs/ragtag/bin/ragtag_scaffold.py", line 555, in main write_orderings(output_path + file_prefix + ".agp", output_path + file_prefix + ".confidence.txt", query_file, mapped_ref_seqs, fltrd_ctg_alns, pad_sizes, gap_types, make_chr0, True, not remove_suffix, skip_no_cat) File "/home/xingbo.wu/.conda/envs/ragtag/bin/ragtag_scaffold.py", line 160, in write_orderings agp.add_seq_line(*out_agp_line) File "/home/xingbo.wu/.conda/envs/ragtag/lib/python3.7/site-packages/ragtag_utilities/AGPFile.py", line 216, in add_seq_line self._add_line(agp_line) File "/home/xingbo.wu/.conda/envs/ragtag/lib/python3.7/site-packages/ragtag_utilities/AGPFile.py", line 139, in _add_line raise AGPError(self.fname, agp_line.line_number, "object identifier out of order") ragtag_utilities.AGPFile.AGPError:

FILE : /lustre/project/gbru/gbru_hydrangea/EndlessSummer/ragtag_ccs/ragtag.scaffold.agp LINE : 412 ERROR: object identifier out of order

Thanks

[malonge]

Hi there,

So the direct error is that RagTag scaffold is trying to write an improperly formatted AGP file. But I can't tell why this is happening in the first place. Would you be open to sharing your data with me so I can reproduce the error on my end? [email protected]

[Sameer1028]

HI Malonge,

I am also facing a similar problem. Your insights would have been very helpful to me.