Troubleshooting
This page is developing based on the user feedback.
Debugging mode
Turn on ‘debugging mode’ (bottom-right button) to keep temporary (log) files for identifying the cause of the error
General
Error
Conflict. The container name XXX is already in use by container “XXX”. You have to remove (or rename) that container to be able to reuse that name.
Reason: Process stopped unexpectedly and docker container was not closed.
Fix: Remove the docker container (not image!) that is causing the conflict
Error
No files in the output folder, but PipeCraft said “Workflow finished”.
Possible reason: Computer’s memory (RAM) is full, and process was killed. Cannot finish the analyses with those local resources.
- Possible fix: In Windows, try to increase the RAM size accessible to Docker (see here).
Check if there was a README.txt output and read that. Please report unexpexted errors.
Error
No OTU_table.txt with version v0.1.4
Reason: known bug.
Fix: Fixed the bug. Reinstall PipeCraft v0.1.4 (or higher)
Error
“ERROR]: cannot find files with specified extension”
Reason: wrongly specified working directory or extension; OR issues with external hard drives in Windows.
Fix: Double-check the specified directory and extention; OR restart Windows.
Error
“Workflow stopped”
Possible reason: Computer’s memory (RAM) is full, and process was killed. Cannot finish the analyses with those local resources.
Possible fix: In Windows, try to increase the RAM size accessible to Docker (see here).
Error
Error in filterAndTrim. Every input file must have a corresponding output file.
Possible reason: wrong read identifiers for read R1 and read R2 in QUALITY FILTERING panel.
Fix: Check the input fastq file names and edit the identifiers. Specify identifyer string that is common for all R1 reads (e.g. when all R1 files have ‘.R1’ string, then enter ‘\.R1’. Note that backslash is only needed to escape dot regex; e.g. when all R1 files have ‘_R1’ string, then enter ‘_R1’.).
Error
“Error rates could not be estimated (this is usually because of very few reads). Error in getErrors(err, enforce = TRUE) : Error matrix is null.”
Possible reason: Too small data set; samples contain too few reads for DADA2 denoising.
Fix: use OTU workflow.