Error related with busco

[anacatarinaas]

Hi,

Does hapsolo only work with busco3? I am having this error when I run hapsolo and maybe is related to the version, in the cluster I have access to they don't have that version and I can't install it myself. What is hapsolo using from busco? Maybe I can try to get the file ready myself?

Thanks for any help you can provide Cheers, Ana

hapsolo.py -t 32 -i Mtar.fasta --paf Mtar_self_align.paf -b busco/

Traceback (most recent call last): File "/shared/home/asilva/HapSolo/hapsolo.py", line 819, in busco2contigdict, contigs2buscodict = importBuscos(buscofileloc) File "/shared/home/asilva/HapSolo/hapsolo.py", line 196, in importBuscos for line in open(mybuscofiles[0]): IndexError: list index out of range

[OZTaekOppa]

Hi,

I am having a similar issue despite the BUSCO3 outcome.

/work/HapSolo/hapsolo.py -i SPO_CN1KCt_RN.fasta --paf /work/HapSolo/MM2/HS1_SPO_Self.paf -b /work/HapSolo/BUSCOTestDef_v4/run_BC_SPOCN1KCT_AllV32 -t 10

I have also tried to indicate as /work/HapSolo/BUSCOTestDef_v4/ but no luck.

Traceback (most recent call last): File "/work/HapSolo/hapsolo.py", line 819, in busco2contigdict, contigs2buscodict = importBuscos(buscofileloc) File "/work/HapSolo/hapsolo.py", line 196, in importBuscos for line in open(mybuscofiles[0]): IndexError: list index out of range

Any suggestion?

Cheers

[sunnycqcn]

Hi,

I am having a similar issue despite the BUSCO3 outcome.

/work/HapSolo/hapsolo.py -i SPO_CN1KCt_RN.fasta --paf /work/HapSolo/MM2/HS1_SPO_Self.paf -b /work/HapSolo/BUSCOTestDef_v4/run_BC_SPOCN1KCT_AllV32 -t 10

I have also tried to indicate as /work/HapSolo/BUSCOTestDef_v4/ but no luck.

Traceback (most recent call last): File "/work/HapSolo/hapsolo.py", line 819, in busco2contigdict, contigs2buscodict = importBuscos(buscofileloc) File "/work/HapSolo/hapsolo.py", line 196, in importBuscos for line in open(mybuscofiles[0]): IndexError: list index out of range

Any suggestion?

Cheers

I met the same issue. Did you know how to solve it? Thanks, Fuyou

[esolares]

Hi unfortunately it does not. I do however have a singularity image with the supported BUSCO version. My apologies for not getting to this earlier. I have been busy with moving and starting my new post doc position. I will work on fixing the bugs as well as adding support for different versions of BUSCO.

[parkgyuhwang]

Change the busco result file name like this : full_table_***.tsv

Chage the busco result file form like this :

# BUSCO version is: 3.0.0
# The lineage dataset is: sample dataset BUSCO 2.0 (Creation date:
07.10.2016, number of species: 23, number of BUSCOs: 10)
# To reproduce this run: python scripts/run_BUSCO.py -i sample_data/target.fa -o TEST -l sample_data/example -m genome -c 1 -f
#
BUSCO_1 Complete sample 30184 31421 320.9 193
BUSCO_2 Complete sample 31646 47625 872.0 443
BUSCO_3 Complete sample 62761 68675 241.8 146

[yschoeneberg]

For me, the issue was resolved by simply changing line 192 in script hapsolo.py from mybuscofiles = glob.glob(buscofileloc + '/busco*/*/full_table_*.tsv') to mybuscofiles = glob.glob(buscofileloc + '/full_table_*.tsv')

[esolares]

Yes you can either create the tsv files or update the line of code so it points to your file. If you do not have a directory of busco1 to buscon directories in your -b argument, it will not find your tsv files.