The run will not start¶
null: command not found¶
Your parameters.config predates the installed version. An absent parameter interpolates as the literal string null, which is why the error names nothing useful and points at a generated script. Rebuild the file (see Upgrading).
Process requirement exceeds available CPUs¶
threads is larger than the machine. Tasks reserve what they really use, so an oversized request fails at submission rather than quietly oversubscribing. Set threads to the cores you have. Resources →
RUN PARAMETERS names a setting that would waste the run¶
RUN PARAMETERS: FAIL variantCall.scaleMapQ: DISCARDS EVERY READ (15 is below varQualMin 30)
RUN PARAMETERS: -C caps every read's mapping quality near 15 and -q then
RUN PARAMETERS: rejects anything under 30, so the pileup reaches bcftools
RUN PARAMETERS: call empty and the run produces no variants at all.
RUN PARAMETERS: A setting above would make this run produce nothing, or stop it partway.
Not the change guard: nothing about your existing results is wrong. A setting in parameters.config would make the run produce no output at all, or stop it partway, and it is being stopped now rather than after the hours of alignment and calling it would waste. The message names the parameter, both values where two interact, and what to change.
WARN and NOTE lines in the same section do not stop anything. A warning means the setting works and costs more than it looks like it does; a note means it changes what a published number means. Only FAIL stops a run. Every rule, and what each level means ->
PoolSeqFlow check project applies the same rules from the same implementation, so you can see all of this before starting.
RUN PARAMETER CHECK or METADATA CHANGE CHECK fails¶
Working as designed. An analysis-affecting parameter, or the analysis-affecting part of metadata.csv, differs from what produced your existing outputs. Because completed steps are skipped by looking for output files, continuing would mix results from two configurations in one folder.
The report names what to delete, and how much that is depends on what you changed. A reordered file invalidates less than an edited tag value, and a changed pool size less again. Deleting what it names clears the check. Or PoolSeqFlow reset to discard everything. Why →
PIPELINE VERSION fails¶
These results were produced by a different release. A project belongs to one release, so this one is absolute: nothing else is compared and there is nothing to delete selectively. Either finish the project under the release that started it (every installed version is on your PATH by its own name) or PoolSeqFlow reset and start again under this one. Why →
METADATA CHECK reports a duplicate SampleID¶
A SampleID appears more than once. A row is looked up by it and only the first match is read, so the duplicate would have silently given a sample the wrong read-group tags, producing a valid BAM that nothing downstream could flag. Every problem in the file is reported at once, with line numbers, so fix the whole list before rerunning.
A sample has reads but no row, and a row has no reads¶
Sample 'A08781_S58' has reads but no row in metadata.csv
NOTE: metadata.csv has a row for 'A08781', which has no reads in Data/
These two lines are one problem, and the answer is the difference between them. One name has files and no row, the other has a row and no files, and they differ by a suffix your sequencer added. Illumina's demultiplexing appends _S<n>, the sample's row number in the sample sheet, so the sample you call A08781 arrives as A08781_S58_R1.fq.gz.
SampleID is what joins a row to its files, so it has to carry the whole delivered name. Lengthen SampleID, and never rename the files. Then put the name you want your results under in RG_Sample:
With sixty samples you get sixty of each line. Listing the identifiers from the files themselves is faster than reading them off a sample sheet:
DIRECTORY CHECK fails¶
mainDir and storageDir are the same path, or one of them is the installation. They are two storage tiers and an output moving from one to the other is what marks it finished, which cannot mean anything if they are one place. The installation is a tool that is replaced wholesale on upgrade, so a project inside it would not survive one. Why →