ERROR: invalid input file given

[Joredb]

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]

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]

((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]

@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]

@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]

@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)

[zhaoqiang2222]

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

[zhaoqiang2222]

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.

[thom-ST]

thank you

[zhaoqiang2222]

这里能说中文吗？

[thom-ST]

no am comfortable with english only

[ilnamkang]

If you are using a Linux server you share with other users, then you may try designating a temporary directory other than the default. For example,

ezaai extract -i <IN_SEQ> -o <OUT_DB> -tmp /tmp

Below is my guess on the issue.
ezaai seems to use "/tmp/ezaai" as a temporary directory by default.

It is likely that, in a Linux server that is shared by many users, if any user runs ezaai for the first time on the server, then "/tmp/ezaai" is created with that user being the owner of the directory.

If you run ezaai afterwards, you cannot create "/tmp/ezaai" because the directory exists already, and you don't have permission to overwrite it. Therefore, ezaai terminates with an error.

If you run ezaai with "-tmp /tmp" option, temporary files and/or directories will be created in /tmp directory, but with file/directory names that do not prohibit other user from running ezaai in their accounts.

[endixk]

Hello all, I just made an update regarding this issue.

First, the program will terminate if a non-writable output or temp directory is given. Thank you @ilnamkang for sharing your observation, which is a critical point that I overlooked.

The error message was ambiguous since extract module calls convert module as a child process. If the prodigal extraction wasn't successful, the program complained about the input file of the convert sub-module, instead of raising error around the erroneous extraction. To mitigate this, the extract module will now check the extraction result before proceeding to the conversion.

I will soon release a new stable version with these updates reflected.