NanoCount: error: unrecognized arguments: NanoCount

[clsgithubusr]

Hello
Our MasterOfPores user is trying to use the NanoCount option in the counter_opt parameters.

But then she received the following error when running her pipeline:

Process `counting (fast5)` terminated with an error exit status (2)

Command executed:

NanoCount -i fast5.minimap2.sorted.bam -o fast5.count NanoCount;
awk '{sum+=$3}END{print FILENAME" "sum}' fast5.count |sed s@.count@@g > fast5.stats
samtools view -F 256 fast5.minimap2.sorted.bam |cut -f 1,3 > fast5.assigned

Command exit status:
2

Command output:
(empty)

Command error:
usage: NanoCount [-h] [--version] -i ALIGNMENT_FILE [-o COUNT_FILE]
[-l MIN_READ_LENGTH] [-f MIN_QUERY_FRACTION_ALIGNED]
[-t EQUIVALENT_THRESHOLD] [-s SCORING_VALUE]
[-c CONVERGENCE_TARGET] [-e MAX_EM_ROUNDS] [-x] [-v] [-q]
NanoCount: error: unrecognized arguments: NanoCount

the NanoCount -i fast5.minimap2.sorted.bam -o fast5.count NanoCount; command is generated from the nanopreprocess.nf file
it is also using the biocorecrg-mopprepr-0.6.img container to run the commands.

[eylenth]

@lucacozzuto or @ADelgadoT , do you have any suggestions on this ?
We will probably need to modify the Nanocount parameter or we need to use another version of the biocorecrg-mopprepr img container.

[ADelgadoT]

Hi,

To use NanoCount in MoP, you don't need to write NanoCount in the counter_opt parameter in the params.config file. MasterOfPores will run NanoCount if you are mapping to the transcriptome and the counter parameter is YES.

Your params.config file should contain the following lines to run NanoCount:

ref_type = "transcriptome"
counter = "YES"

The parameter counter_opt is used to introduce additional parameters to NanoCount command, for example, to only take into account primary alignments, etc. [https://adrienleger.com/NanoCount/NanoCount_CLI_usage/].

I can run NanoCount with MoP when using these options - tell me if it works for you too.

Thanks,

Anna

[eylenth]

Hi Anna

THe end user reported that is now working for her with those settings.

The ticket can be closed.