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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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ERROR, skch::validateInputFiles #88

Open analopezlopez opened 2 years ago

analopezlopez commented 2 years ago

Hi,

I'm trying to use the many to many option of FastANI for the first time and I keep getting this message:

ERROR, skch::validateInputFiles, Could not open /home/analopez/snic2020-6-60/AnaLopez/squeezemeta/coassembly_mode/RUN_3new/results/DAS/RUN3_new_DASTool_bins/maxbin.002.fasta.contigs.fa

Is it .fa not a valid extension, maybe? Or is there something else going on?

Thank you in advance, Ana

cjain7 commented 2 years ago

No issue with .fa extension. It is likely that the executable is unable to access / read the file at the path you gave /home/analopez/snic2020-6-60/AnaLopez/squeezemeta/coassembly_mode/RUN_3new/results/DAS/RUN3_new_DASTool_bins/maxbin.002.fasta.contigs.fa

Double check the file path.

MichaelRyanUL commented 1 year ago

Hi

I am having a very similar issue

fastANI -q UL_CPE_C1.fna --rl genome.txt -o Citrobacter_ANI.tsv

Reference = [Citrobacter_amalonaticus_FDAARGOS_165.fna, Citrobacter_arsenatis_LY-1.fna, Citrobacter_braakii_MiY-A.fna, Citrobacter_cronae _S175-1.fna, Citrobacter_europaeus_FDAARGOS_1490.fna, Citrobacter_farmeri_FDAARGOS_1423.fna, Citrobacter_freundii_FDAARGOS_549.fna, Citrobacter_koseri_ATCCBAA-895.fna, Citrobacter_murliniae.fna, Citrobacter_pasteurii_FDAARGOS_1424.fna, Citrobacter_portucalensis_FDAARGOS_617.fna, Citrobacter_rodentium_NBRC105723.fna, Citrobacter_sedlakii _3347689II.fna, Citrobacter_telavivensis_6105.fna, Citrobacter_tructae_SNUWT2.fna, Citrobacter_werkmanii_FDAARGOS_616.fna, Citrobacter_youngae_NCTC13709.fna] Query = [UL_CPE_C1.fna] Kmer size = 16 Fragment length = 3000 Threads = 1 ANI output file = Citrobacter_ANI.tsv

ERROR, skch::validateInputFiles, Could not open Citrobacter_amalonaticus_FDAARGOS_165.fna

I have tried everything I can think of but no luck. Any help would be appreciated

Kind Regards, Michael