Error submitting process

[wangzhiwei-sd]

The command we use is: nextflow run PATH/ardap/main.nf --executor pbs --fastq "empty_reads/*_{1,2}.fastq.gz" --assemblies true --species Pseudomonas_aeruginosa --notrim true

We encountered errors when running a Nextflow pipeline (ardap/main.nf) for Pseudomonas aeruginosa genome prediction using pre-assembled FASTA files in the assemblies folder. Initial attempts failed until empty FASTQ files were added via --fastq "empty_reads/*_{1,2}.fastq.gz", allowing partial execution but resulting in persistent errors：

[dc/52860b] NOTE: Error submitting process 'Trimmomatic (dummy)' for execution -- Execution is retried (4)
[1f/cea63f] NOTE: Error submitting process 'Read_synthesis (GCA_025108165.2)' for execution -- Execution is retried (4)
[07/9131e2] NOTE: Error submitting process 'Read_synthesis (GCA_025126655.2)' for execution -- Execution is retried (4)
[47/996064] NOTE: Error submitting process 'Read_synthesis (GCA_025126635.2)' for execution -- Execution is retried (4)
[57/e4e683] NOTE: Error submitting process 'Read_synthesis (GCA_025108225.2)' for execution -- Execution is retried (4)

Can you help me with this? Thank you.

[dsarov]

This is a known limitation, my apologies. The easiest way to fix it is to just feed in some fastq reads so the program can run those as well as assemblies. I'll see if I can improve the code though and let you know. Shouldn't be too difficult to alter the logic in the pipeline to run without fastq files.

[wangzhiwei-sd]

We would like to test the integration of some FASTQ reads and then proceed with the execution. Once the code has been modified and is ready, could you kindly inform us? We greatly appreciate the excellent software you have provided. Thank you.