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dfguan / purge_dups

haplotypic duplication identification tool
MIT License
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ERROR: run_busco2 failed, return code: 127 #146

Open rmormando opened 4 months ago

rmormando commented 4 months ago

I am trying to run the purge_dups pipeline using run_purge_dups.py but for some reason I keep getting this error:

calculate coverage and self-alignment
command src/split_fa /Users/rimo/PURGE_DUPS/purge_dups/sample_combHIFIASM/Saccharomyces_cerevisiae_OG.fasta > Saccharomyces_cerevisiae_OG/split_aln/Saccharomyces_cerevisiae_OG.split.fa run successfully
command minimap2 -I 4G -x map-pb -t 12 /Users/rimo/PURGE_DUPS/purge_dups/sample_combHIFIASM/Saccharomyces_cerevisiae_OG.fasta /Volumes/TheDatabase/PACBIO_WORK/sample_pbHIFI2_hifiasm_primary/sample_pbHIFI2.asm.combined.fasta >Saccharomyces_cerevisiae_OG/coverage/sample_pbHIFI2.asm.combined.paf run successfully
command src/pbcstat -O Saccharomyces_cerevisiae_OG/coverage Saccharomyces_cerevisiae_OG/coverage/sample_pbHIFI2.asm.combined.paf run successfully
command minimap2 -xasm5 -DP Saccharomyces_cerevisiae_OG/split_aln/Saccharomyces_cerevisiae_OG.split.fa Saccharomyces_cerevisiae_OG/split_aln/Saccharomyces_cerevisiae_OG.split.fa > Saccharomyces_cerevisiae_OG/split_aln/Saccharomyces_cerevisiae_OG.split.paf run successfully
command src/calcuts  Saccharomyces_cerevisiae_OG/coverage/PB.stat > Saccharomyces_cerevisiae_OG/coverage/cutoffs run successfully
purge duplicates
command src/purge_dups -2 -c Saccharomyces_cerevisiae_OG/coverage/PB.base.cov -T Saccharomyces_cerevisiae_OG/coverage/cutoffs Saccharomyces_cerevisiae_OG/split_aln/Saccharomyces_cerevisiae_OG.split.paf > Saccharomyces_cerevisiae_OG/purge_dups/dups.bed run successfully
command src/get_seqs -e -p Saccharomyces_cerevisiae_OG/seqs/Saccharomyces_cerevisiae_OG Saccharomyces_cerevisiae_OG/purge_dups/dups.bed /Users/rimo/PURGE_DUPS/purge_dups/sample_combHIFIASM/Saccharomyces_cerevisiae_OG.fasta run successfully
command run_busco2 Saccharomyces_cerevisiae_OG.purged.fa 12 Saccharomyces_cerevisiae_OG_purged  busco_tmp failed, return code: 127
command minimap2 -I 4G -x map-pb -t 12 Saccharomyces_cerevisiae_OG/seqs/Saccharomyces_cerevisiae_OG.purged.fa /Volumes/TheDatabase/PACBIO_WORK/sample_pbHIFI2_hifiasm_primary/sample_pbHIFI2.asm.combined.fasta >Saccharomyces_cerevisiae_OG/seqs/cal_cov/sample_pbHIFI2.asm.combined.paf run successfully
unkown error, please check error log
command src/pbcstat -O Saccharomyces_cerevisiae_OG/seqs/cal_cov Saccharomyces_cerevisiae_OG/seqs/cal_cov/sample_pbHIFI2.asm.combined.paf run successfully
command src/calcuts  Saccharomyces_cerevisiae_OG/seqs/cal_cov/PB.stat > Saccharomyces_cerevisiae_OG/seqs/cal_cov/cutoffs failed, return code: 136
unkown error, please check error log

I used this command to make the config file: python3 scripts/pd_config.py -l sample_combHIFIASM -n sample_combHIFIASM_purgeDUPS_config.json /Users/rimo/data/Saccharomyces_cerevisiae_OG.fasta sample_combinedHIFIASM.fofn

and this command to run the pipeline: python3 scripts/run_purge_dups.py -p bash sample_combHIFIASM_purgeDUPS_config.json src sample_combHIFIASM

I traced where purge_dups calls BUSCO in the run_busco.py script and it should be using version 3.0.2 from quast_libs.busco import busco which you can verify here: https://github.com/ablab/quast/blob/master/quast_libs/busco/_version.py

Can someone please explain why this is happening and a solution to get this to run?