paulonvnv/mhap-analysis

Amplicon sequencing analysis of Colombian data set

mhap-analysis's Issues

Issue with AmpliconPipeline.py filtering samples

There is an issue with AmpliconPipeline.py when I execute it at the step of filtering the samples (I used every vivax sample in the repository), where it only goes up to making the qualityR and qualityF images and fails before producing zeroReadSamples, error rates plots, Bimera tables, reads summary, and seqtab.

the error message in stderr is:

Warning message:
package ‘argparse’ was built under R version 3.6.3 
Loading required package: Rcpp
Warning message:
package ‘Rcpp’ was built under R version 3.6.3 
Warning message:
package ‘data.table’ was built under R version 3.6.3 
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
The filter removed all reads: /mnt/c/Users/mm/Desktop/malaria-amplicon-pipeline-main/run_dada2/filtered/HRP0170-R1_S50_filt_R1.fastq.gz and /mnt/c/Users/mm/Desktop/malaria-amplicon-pipeline-main/run_dada2/filtered/HRP0170-R1_S50_filt_R2.fastq.gz not written.
Error in names(answer) <- names1 : 
  'names' attribute [74] must be the same length as the vector [55]
Calls: filterAndTrim -> mcmapply
In addition: Warning message:
In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule,  :
  scheduled cores 2, 6, 9 did not deliver results, all values of the jobs will be affected
Execution halted

I'm using Ubuntu: Ubuntu 22.04.3 LTS and R 3.6.1

Thanks