endixk/ezaai

ERROR: invalid input file given

Opened this issue · 10 comments

Joredb commented

Hi,
I installed Ezaai using conda. However, there is an error when running the command as shown below:

Command: ezaai extract -i fasta/Ci.fasta -o db/seq_db -dev
[MAR 13 17:12:16] EzAAI |: EzAAI - v1.2.3 [Feb. 2024]
[MAR 13 17:12:16] EzAAI |: Checking dependencies...
[MAR 13 17:12:16] DEV |: exec: prodigal -h
[MAR 13 17:12:17] DEV |: exec: mmseqs -h
[MAR 13 17:12:17] DEV |: EzAAI - extract module
[MAR 13 17:12:17] EzAAI |: Running prodigal on genome fasta/Ci.fasta...
[MAR 13 17:12:17] DEV |: exec: prodigal -i fasta/Ci.fasta -f gff -o /tmp/ezaai/aefac6c266baa84a.gff -a /sample/fasta/Ci.fasta.faa -d /tmp/ezaai/aefac6c266baa84a.ffn -q -p meta -g 11
[MAR 13 17:12:17] EzAAI |: Creating a submodule for converting .faa into .db...
[MAR 13 17:12:17] ERROR |: Invalid input file given.
[MAR 13 17:12:17] ERROR |: Program terminated with error.

How to solve this issue?
Thanks.

endixk commented

Hi, sorry for the late reply.

Seems like the prodigal did not run properly and failed to produce CDS FASTA file.

You might be able to find the underlying error of prodigal by examining the output from this sub-command:

prodigal -i fasta/Ci.fasta -f gff -o /tmp/ezaai/aefac6c266baa84a.gff -a /sample/fasta/Ci.fasta.faa -d /tmp/ezaai/aefac6c266baa84a.ffn -q -p meta -g 11
thom-ST commented

((base) mahe@pop-os:/Downloads/PhD/Automation Trial/Automation scripts/AAI&ANI/sample/fasta$ ezaai extract -i Cn.fasta -o Cn.db -l "Clavibacter nebraskensis"
[MAY 28 11:09:46] EzAAI |: EzAAI - v1.2.3 [Feb. 2024]
[MAY 28 11:09:47] EzAAI |: Running prodigal on genome Cn.fasta...
[MAY 28 11:09:47] ERROR |: Invalid input file given.
[MAY 28 11:09:47] ERROR |: Program terminated with error.
(base) mahe@pop-os:/Downloads/PhD/Automation Trial/Automation scripts/AAI&ANI/sample/fasta$ prodigal -i fasta/Ci.fasta -f gff -o /tmp/ezaai/aefac6c266baa84a.gff -a /sample/fasta/Ci.fasta.faa -d /tmp/ezaai/aefac6c266baa84a.ffn -q -p meta -g 11

Error: can't open input file fasta/Ci.fasta.
same error i got i tried with above sub-command also

endixk commented

@thom-ST Hello,

Could you please check if your input file paths are valid?
You can try to use an absolute path (starting from /) to make sure your input path is correct.

thom-ST commented

@endixk (base) mahe@pop-os:/Downloads/PhD/Automation Trial/Automation scripts/AAI&ANI/sample$ ezaai extract -i Ci.fasta -o ci.db
[JUN 03 12:52:08] EzAAI |: EzAAI - v1.2.3 [Feb. 2024]
[JUN 03 12:52:08] EzAAI |: Running prodigal on genome Ci.fasta...
[JUN 03 12:52:08] ERROR |: Invalid input file given.
[JUN 03 12:52:08] ERROR |: Program terminated with error.
(base) mahe@pop-os:/Downloads/PhD/Automation Trial/Automation scripts/AAI&ANI/sample$ ezaai extract -i /home/mahe/Downloads/PhD/Automation\ Trial/Automation\ scripts/AAI&ANI/sample/Ci.fasta -o /home/mahe/Downloads/PhD/Automation\ Trial/Automation\ scripts/AAI&ANI/sample/ci.db
[JUN 03 12:53:19] EzAAI |: EzAAI - v1.2.3 [Feb. 2024]
[JUN 03 12:53:19] EzAAI |: Running prodigal on genome /home/mahe/Downloads/PhD/Automation Trial/Automation scripts/AAI&ANI/sample/Ci.fasta...
[JUN 03 12:53:19] ERROR |: Invalid input file given.
[JUN 03 12:53:19] ERROR |: Program terminated with error.
(base) mahe@pop-os:~/Downloads/PhD/Automation Trial/Automation scripts/AAI&ANI/sample$
i used the sample data only

thom-ST commented

@endixk But in WSL , it was working in fine i cant process batch files..for calculate.. i want to understand why its not running on Popos (linux)

  • 👍1
zhaoqiang2222 commented

I got the same problem like above, only in WSL, it works.

zhaoqiang2222 commented

I have got the reason of this problem, because I don't have the sudo right of the computer, so I can't write in files at /tmp.

  • ❤️1
thom-ST commented

thank you

zhaoqiang2222 commented

这里能说中文吗？

thom-ST commented

no am comfortable with english only