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schmeing / gapless

Gapless provides combined scaffolding, gap-closing and assembly correction with long reads
MIT License
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AttributeError: 'DataFrame' object has no attribute 'append' #11

Open chenzhao12 opened 1 year ago

chenzhao12 commented 1 year ago

gapless.py extend -p gapless gapless_extending_reads.paf 0:00:15.342579 Preparing data from files 0:13:51.708704 Searching for extensions Traceback (most recent call last): File "/home/zhuchenzhao/miniconda3/bin/gapless.py", line 13327, in main(sys.argv[1:]) File "/home/zhuchenzhao/miniconda3/bin/gapless.py", line 13193, in main GaplessExtend(args[0], prefix, min_length_contig_break) File "/home/zhuchenzhao/miniconda3/bin/gapless.py", line 9610, in GaplessExtend scaffold_paths, polishing_reads, extension_info, gap_scaffolds = ExtendScaffolds(scaffold_paths, polishing_reads, extensions, hap_merger, new_scaffolds, mappings, min_num_reads, max_mapping_uncertainty, min_scaf_len, ploidy, polishing_coverage) File "/home/zhuchenzhao/miniconda3/bin/gapless.py", line 9515, in ExtendScaffolds scaffold_paths = scaffold_paths.append( extending_reads[['scaf','pos','type']+[f'{n}{h}' for h in range(ploidy) for n in ['phase','name','start','end','strand']]+['sdist_left','sdist_right']] ) File "/home/zhuchenzhao/miniconda3/lib/python3.9/site-packages/pandas/core/generic.py", line 5989, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'append'

JhinAir commented 1 year ago

same issue here. Has it been solved?

JhinAir commented 1 year ago

It's an issue of 'pipeline crashed: extend'. Could you please help check it out?@schmeing

ashleyp1 commented 1 year ago

I also just experienced this same issue

bennuru commented 12 months ago

The 'append' issue is probably related to pandas version. Try with pandas 1.5.3 as 'append' has been removed from pandas>=2.0.

YocelynG commented 10 months ago

I ran into the same error. It looks like some files did not generated in the previous steps. I fixed it by running the pipeline step by step with some modifications:

gapless.py split -o gapless_split.fa assembly_hifiasm_ctg.fasta minimap2 -t 30 -DP -k19 -w19 -m200 gapless_split.fa gapless_split.fa > gapless_split_repeats.paf minimap2 -t 30 -x map-hifi -c -N 5 --secondary=no gapless_split.fa hifi_reads.default.filt.fastq.gz > gapless_reads.paf gapless.py scaffold -p gapless -s gapless_stats.pdf gapless_split.fa gapless_reads.paf gapless_split_repeats.paf minimap2 -t 30 -x map-hifi <(seqtk subseq hifi_reads.default.filt.fastq.gz gapless_extending_reads.lst) <(seqtk subseq hifi_reads.default.filt.fastq.gz gapless_extending_reads.lst) > gapless_extending_reads.paf gapless.py extend -p gapless gapless_extending_reads.paf seqtk subseq hifi_reads.default.filt.fastq.gz gapless_used_reads.lst > temp_finish.fastq

Here the option -p is not indicated in the documentation

gapless.py finish -o gapless_raw.fa -H 0 -s gapless_extended_scaffold_paths.csv -p gapless_polishing.csv gapless_split.fa temp_finish.fastq minimap2 -t 30 -x map-hifi gapless_raw.fa hifi_reads.default.filt.fastq.gz > gapless_consensus.paf racon -t 30 hifi_reads.default.filt.fastq.gz gapless_consensus.paf gapless_raw.fa > gapless.fa