Unable to obtain final report for simple assembly pipeline #220
Description
I have created a simple assembly pipeline that downloads Streptococcus agalactiae reads from SRA by providing an accession number and processes reads in order to get assemblies that have passed certain quality control steps. To create the pipeline I used the following command:
flowcraft build -t "reads_download downsample_fastq integrity_coverage fastqc_trimmomatic check_coverage fastqc spades assembly_mapping pilon mlst" -o simple_innuca.nf
The process seems to progress normally and the commands flowcraft inspect -m broadcast and flowcraft report -w allow me to follow the pipeline progress and interpret results for each sample as they become available. My issue shows up at the end when all samples have been processed and I should get the final report. I get this output:
[18/29fb6f] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (1)
[ee/80c500] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (2)
[4e/0d6bb0] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (3)
[11/f224b1] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (4)
[74/db3e0a] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (5)
[c8/5e36ac] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (6)
[e7/54ce70] NOTE: Error submitting process 'compile_reports (1)' for execution -- Execution is retried (7)
[49/048771] NOTE: Error submitting process 'compile_reports (1)' for execution -- Error is ignored
[52/22be34] Submitted process > compile_status
The process hangs and I need to forcefully stop it. I do not get the final report but I can save the folders with the assemblies and MLST results for the samples that could be processed. This problem does not occur every time I use this pipeline and I managed to get the final report in cases with less SRA reads to process. I'm using Nextflow v18.10.1 and Flowcraft v1.4.2.