Closed wshuai294 closed 8 months ago
Thanks for the amazing tool. I met this error whiling scaffolding, could you help me with this? Here is the log:
Fri Jan 19 21:07:55 2024 --- VERSION: RagTag v2.1.0 Fri Jan 19 21:07:55 2024 --- CMD: ragtag.py scaffold -o segment_result//ragtag_DRR198803 /mnt/d/breakpoints/assembly/sim/database/Escherichia_coli/NZ_CP028685.1.fasta segment_result//DRR198803.split.fasta Fri Jan 19 21:07:55 2024 --- 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'. Fri Jan 19 21:07:55 2024 --- INFO: Mapping the query genome to the reference genome Fri Jan 19 21:07:55 2024 --- INFO: Retaining pre-existing file: /home/wangshuai/assembly_result_v2/segment_result/ragtag_DRR198803/ragtag.scaffold.asm.paf Fri Jan 19 21:07:55 2024 --- INFO: Reading whole genome alignments Fri Jan 19 21:07:55 2024 --- INFO: Filtering and merging alignments Fri Jan 19 21:07:55 2024 --- INFO: Ordering and orienting query sequences Fri Jan 19 21:07:55 2024 --- INFO: Writing scaffolds Fri Jan 19 21:07:55 2024 --- INFO: Writing: /home/wangshuai/assembly_result_v2/segment_result/ragtag_DRR198803/ragtag.scaffold.agp Traceback (most recent call last): File "/home/wangshuai/assembly_result/my_assembly/bin/ragtag_scaffold.py", line 577, in <module> main() File "/home/wangshuai/assembly_result/my_assembly/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/wangshuai/assembly_result/my_assembly/bin/ragtag_scaffold.py", line 211, in write_orderings agp.add_seq_line(*out_agp_line) File "/home/wangshuai/assembly_result/my_assembly/lib/python3.6/site-packages/ragtag_utilities/AGPFile.py", line 215, in add_seq_line agp_line = AGPSeqLine(self.fname, line_number, obj, obj_beg, obj_end, pid, comp_type, comp, comp_beg, comp_end, orientation) File "/home/wangshuai/assembly_result/my_assembly/lib/python3.6/site-packages/ragtag_utilities/AGPFile.py", line 412, in __init__ super(AGPSeqLine, self).__init__(fname, line_number, obj, obj_beg, obj_end, pid, comp_type) File "/home/wangshuai/assembly_result/my_assembly/lib/python3.6/site-packages/ragtag_utilities/AGPFile.py", line 361, in __init__ self._validate_numerics() File "/home/wangshuai/assembly_result/my_assembly/lib/python3.6/site-packages/ragtag_utilities/AGPFile.py", line 449, in _validate_numerics raise AGPError(self.fname, self.line_number, "encountered an invalid zero or negative numeric AGP field.") ragtag_utilities.AGPFile.AGPError: FILE : /home/wangshuai/assembly_result_v2/segment_result/ragtag_DRR198803/ragtag.scaffold.agp LINE : 207 ERROR: encountered an invalid zero or negative numeric AGP field.
solved after removing the existing output files.
Thanks for the amazing tool. I met this error whiling scaffolding, could you help me with this? Here is the log: