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dfguan / purge_dups

haplotypic duplication identification tool
MIT License
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run_busco2 failed return code:127 #119

Open olechnwin opened 2 years ago

olechnwin commented 2 years ago

Hi, I am trying to run_purge_dups .py but it failed when it tries to run_busco2. I saw inside run_busco2 there are many paths that are specific to your folder. I think I'm supposed to change this to my paths. Does that mean I need to install busco, Augustus, etc? Also I don't see run_BUSCO.py anywhere in the repo. I am confused on how I'm supposed to modify run_busco2. Please let me know. Thank you in advance.

+ python /home/gdlessnicklab/cxt050/opt/purge_dups/scripts/run_purge_dups.py -p bash config.json /home/gdlessnicklab/cxt050/opt/purge_dups/src a673_hifi_bionano_hic
calculate coverage and self-alignment
command /home/gdlessnicklab/cxt050/opt/purge_dups/src/split_fa /gpfs0/home1/gdlessnicklab/cxt050/Data/A673_bionano/output/hybridscaffold_hifiasm_hap1/hybrid_scaffolds/scaffolds/scaffolds_FINAL.fasta > scaffolds_FINAL/split_aln/scaffolds_FINAL.split.fa run successfully
command minimap2 -xasm5 -DP scaffolds_FINAL/split_aln/scaffolds_FINAL.split.fa scaffolds_FINAL/split_aln/scaffolds_FINAL.split.fa > scaffolds_FINAL/split_aln/scaffolds_FINAL.split.paf run successfully
command minimap2 -I 4G -x asm20 -t 12 /gpfs0/home1/gdlessnicklab/cxt050/Data/A673_bionano/output/hybridscaffold_hifiasm_hap1/hybrid_scaffolds/scaffolds/scaffolds_FINAL.fasta /home/gdlessnicklab/cxt050/Data/A673_pacbio/HiFi/fastq/A673_HiFi_CCS.4-cells.fastq.gz >scaffolds_FINAL/coverage/A673_HiFi_CCS.4-cells.fastq.paf run successfully
command /home/gdlessnicklab/cxt050/opt/purge_dups/src/pbcstat -O scaffolds_FINAL/coverage scaffolds_FINAL/coverage/A673_HiFi_CCS.4-cells.fastq.paf run successfully
command /home/gdlessnicklab/cxt050/opt/purge_dups/src/calcuts  scaffolds_FINAL/coverage/PB.stat > scaffolds_FINAL/coverage/cutoffs run successfully
purge duplicates
command /home/gdlessnicklab/cxt050/opt/purge_dups/src/purge_dups -2 -c scaffolds_FINAL/coverage/PB.base.cov -T scaffolds_FINAL/coverage/cutoffs scaffolds_FINAL/split_aln/scaffolds_FINAL.split.paf > scaffolds_FINAL/purge_dups/dups.bed run successfully
command /home/gdlessnicklab/cxt050/opt/purge_dups/src/get_seqs -e -p scaffolds_FINAL/seqs/scaffolds_FINAL scaffolds_FINAL/purge_dups/dups.bed /gpfs0/home1/gdlessnicklab/cxt050/Data/A673_bionano/output/hybridscaffold_hifiasm_hap1/hybrid_scaffolds/scaffolds/scaffolds_FINAL.fasta run successfully
command run_busco2 scaffolds_FINAL.purged.fa 12 scaffolds_FINAL_purged vertebrata busco_tmp failed, return code: 127
unkown error, please check error log
jacquelinemattos commented 2 years ago

Hi, Having the same problem here. Any help would be appreciated.

Thanks, Jacqueline

olechnwin commented 2 years ago

@mattosjacq, run_busco.py came from BUSCO so you would need to install BUSCO version 3. Version 5 of BUSCO does not have run_busco.py After installing BUSCO, I set the path in config.ini following the instruction in BUSCO. I was able to run purge_dups without having to change run_busco2 at all.

Hope that helps.

jacquelinemattos commented 2 years ago

Hi, @olechnwin

Thank you so much for your help. I'll give that a try!

Cheers,

ilikvlad commented 2 years ago

@olechnwin Hi, I have the same issue, unfortunately this did not work for me: May I ask, how exactly did you use the config.ini? And what version of BUSCO did you use? I installed 3.0.2 and it's not working.

Any advice will be appreciated.

Thanks,

Vladislav

rmormando commented 6 months ago

this is happening to me as well...did a solution ever get figured out?