Tracing issues with racon after running mini_assemble

[beasty1711]

Is there any way of tracking/ tracing issues with racon thats included in Pomoxis?

I'm getting "[racon::Polisher::initialize] error: empty target sequences set!" after running mini_assemble.

[cjw85]

Hi @beasty1711

Can you provide the full command you are running (mini_assemble has several modes of operation), and the full log of its output?

[beasty1711]

Hi,

Thanks for getting back to me, the command is:

mini_assemble -i ~/data/filtered/combined_filtered.fq -o denovo -p barcode09_denovo -t 14 -c

Where about's would I find the full log? (I'm the IT guy helping the scientist so not fully aware of the program specifics)

[cjw85]

A lot of information is written to stderr and stdout of the programs which mini_assemble runs. Admittedly its a little daunting to trace back through that for the uninitiated. If you (or your user) can run the program again and redirect stdout and stderr to a file, we can take a look at that.

Your error would indicate that one stage of the pipeline has ended up filtering all the data, we should definitely catch that and report a more interpretable error, at the earliest opportunity. We can guess at a fix but can't guarantee that's going to resolve your particular issue.

[beasty1711]

A lot of information is written to stderr and stdout of the programs which mini_assemble runs. Admittedly its a little daunting to trace back through that for the uninitiated. If you (or your user) can run the program again and redirect stdout and stderr to a file, we can take a look at that.

Your error would indicate that one stage of the pipeline has ended up filtering all the data, we should definitely catch that and report a more interpretable error, at the earliest opportunity. We can guess at a fix but can't guarantee that's going to resolve your particular issue.

Sorry for the long time in responding. The scientist has now gotten further, but receives the attached. Is there any documentation for the tool-set for debugging issues such as this?

[cjw85]

We are currently updating the documentation, and will add an FAQ section.

We have seen this error when the third party racon program is given a sequence file in the fasta format with file extensions usually used for the fastq format (or vice versa). The programs run by mini_assemble before the racon step are not as strict in this regard.

Can you ask your user to check their input has the correct file extension given its format?

[JoannaTan]

Hi,

We are currently using Pomoxis to perform de novo assembly. However, we are also getting the following issue:

racon::createPolisher] error: file A_denovo_trimmed.fa.gz has unsupported format extension (valid extensions: .fasta, .fa, .fastq, .fq)!

This is the command that we used

mini_assemble -i A.fastq -o A_denovo -p A_denovo -t 16 -c

All our input files are in .fastq format.