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B-UMMI / chewBBACA_tutorial

Step by step tutorial using chewBBACA with all necessary files and results
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Error in AlleleCall tutorial #4

Closed Akllarena closed 5 years ago

Akllarena commented 5 years ago

Heisann guys.

I am doing running the chewbacca in a conda environment (tried to downloaded chewbbaca both by conda and pip), and have basically copy pasted all your commands etc. I encounter error msg when running allelcall:

^MProcessing GCA-000007265-protein10.fasta. Start 22:19:33-22/07/2019 Locus 2 of 3130. Done 0%.some error occu$ %i format: a number is required, not NoneType Error on line 466

It is numerous times for most loci and results in non-valid error allele assignments. I went into the schema_seed and had a look at the different loci too, they just look normal. what am I doing wrong?

AK

mickaelsilva commented 5 years ago

should be something related to software versions I guess.

prodigal and blast versions? python version?

Akllarena commented 5 years ago

chewBBACA-2.0.17.1 blast+/2.6.0 prodigal/2.6.1 conda version : 4.5.11 python version : 2.7.15.final.0

I checked the dependencies and they should be ok. Do I have too old python maybe? I can download (or rather load the module python 3.5.1 as I am working on a cluster).

mickaelsilva commented 5 years ago

it works with python 3, not 2, might be that the issue :)

Akllarena commented 5 years ago

Hei, yes, it worked after spec right python version to my conda environment! Thanks.

vvunderkin commented 5 years ago

i'm having the same issue. :(

chewBBACA 2.0.17.1 blast 2.5.0 prodigal 2.6.3 conda 4.7.11 python 3.7.3

mickaelsilva commented 5 years ago

@jeremiahyarmie have you tried with the tutorial dataset?

vvunderkin commented 5 years ago

yes the tutorial dataset is the one that is failing. i can try recloning the repo and trying a fresh conda env. will report back

vvunderkin commented 5 years ago

this is my output

''' etc......

%i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 some error occurred %i format: a number is required, not NoneType Error on line 466 Finished Allele Calling at : 09:53:41-28/08/2019 Wrapping up the results ################################################## 32 genomes used for 3130loci

used a bsr of : 0.6

18908 exact matches found out of 100160

18.87779552715655 percent of exact matches ##################################################

Writing output files

Genome EXC INF LNF PLOT NIPH ALM ASM GCA_000007265.1_ASM726v1_genomic.fna 2442 0 688 0 0 0 0 GCA_000012705.1_ASM1270v1_genomic.fna 2349 0 780 0 1 0 0 GCA_000196055.1_ASM19605v1_genomic.fna 2299 0 789 0 42 0 0 GCA_000299135.1_ASM29913v1_genomic.fna 2254 0 876 0 0 0 0 GCA_000302475.2_ASM30247v2_genomic.fna 2058 0 1072 0 0 0 0 GCA_000427035.1_09mas018883_genomic.fna 2392 0 738 0 0 0 0 GCA_000427055.1_ILRI112_genomic.fna 2240 0 889 0 1 0 0 GCA_000427075.1_ILRI005_genomic.fna 2353 0 777 0 0 0 0 GCA_000599965.1_ASM59996v1_genomic.fna 2038 0 1091 0 1 0 0 GCA_000636115.1_ASM63611v1_genomic.fna 2035 0 1094 0 1 0 0 GCA_000689235.1_GBCO_p1_genomic.fna 2287 0 842 0 1 0 0 GCA_000730215.2_ASM73021v2_genomic.fna 2490 0 640 0 0 0 0 GCA_000730255.1_ASM73025v1_genomic.fna 2321 0 808 0 1 0 0 GCA_000782855.1_ASM78285v1_genomic.fna 2301 0 829 0 0 0 0 GCA_000831105.1_ASM83110v1_genomic.fna 2392 0 733 0 5 0 0 GCA_000831125.1_ASM83112v1_genomic.fna 2391 0 732 0 7 0 0 GCA_000831145.1_ASM83114v1_genomic.fna 2420 0 704 0 6 0 0 GCA_000967445.1_ASM96744v1_genomic.fna 2038 0 1091 0 1 0 0 GCA_001026925.1_ASM102692v1_genomic.fna 2323 0 807 0 0 0 0 GCA_001190805.1_ASM119080v1_genomic.fna 2254 0 875 0 1 0 0 GCA_001190825.1_ASM119082v1_genomic.fna 2251 0 878 0 1 0 0 GCA_001190845.1_ASM119084v1_genomic.fna 2251 0 878 0 1 0 0 GCA_001190865.1_ASM119086v1_genomic.fna 2038 0 1091 0 1 0 0 GCA_001190885.1_ASM119088v1_genomic.fna 2361 0 769 0 0 0 0 GCA_001266635.1_ASM126663v1_genomic.fna 2248 0 882 0 0 0 0 GCA_001275545.2_ASM127554v2_genomic.fna 2330 0 792 0 8 0 0 GCA_001448985.1_ASM144898v1_genomic.fna 2372 0 752 0 6 0 0 GCA_001552035.1_ASM155203v1_genomic.fna 2291 0 838 0 1 0 0 GCA_001592385.1_ASM159238v1_genomic.fna 2328 0 801 0 1 0 0 GCA_001592425.1_ASM159242v1_genomic.fna 2236 0 893 0 1 0 0 GCA_001655175.1_ASM165517v1_genomic.fna 2065 0 1065 0 0 0 0 GCA_001683515.1_ASM168351v1_genomic.fna 2329 0 800 0 1 0 0 checking the existance of paralog genes... Detected number of paralog loci: 2780

Starting Script at : 09:38:46-28/08/2019 Finished Script at : 09:53:41-28/08/2019 '''

mickaelsilva commented 5 years ago

Can you try to update your blast?

than9th commented 5 years ago

same issue as @jeremiahyarmie

chewBBACA 2.0.17.1 blast 2.9.0 prodigal 2.6.3 conda 4.6.14 python 3.7.3

Can you try to update your blast?

rfm-targa commented 5 years ago

@than9th Please try to update chewBBACA to the latest version, 2.0.17.2. And tell me what's the BioPython version you have installed, please. This issue is similar to this issue, that was already closed in the main repository of chewBBACA.

than9th commented 5 years ago

@than9th Please try to update chewBBACA to the latest version, 2.0.17.2. And tell me what's the BioPython version you have installed, please. This issue is similar to this issue, that was already closed in the main repository of chewBBACA.

Thanks. it works with the 2.0.17.2, and the biopython was updated to 1.74.