Help

Alert:

Some users reported an error in the main log file (exampleFQrun.log) while running the fastq test sample (2369):

ERROR: CREATION OF PERSONALIZED PROTEOMES FAILED

The error was caused by an incomplete command line in the Manual, which was missing the -rna argument. Please correct your command as follow:

./NeoDisc.sh RunPipeline \
     fastq \
         -p 2369 \
         -t 2369-tumor \
         -g 2369-germline \
         -rna 2369-tumor \
         -c /path/to/2369.config \
         -runid exampleFQrun \
         -cpu 24 2>&1 | tee exampleFQrun.log

Also, please download the new version of:

NeoDisc Manual

FAQ

Because of the complexity of the pipeline, most errors are caused by incorrect command line, path to the data, configuration file, or formatting of the data. In case of an error, please start by looking at those.

Next, please look at the log files provided by NeoDisc (in the log folders), starting with the most recent one.

NeoDisc does not start and displays the help message

The command provided to NeoDisc is incorrect. Locate the line COMMAND LINE: within the PIPELINE SUBMISSION INFORMATION section in the log to find the error in your command line.

Locate where an error occurs

1. Start by looking at the main log from NeoDisc (e.g. exampleFQrun.log) and identify in which module NeoDisc failed.
2. Find the log file for that module, within the NeoDisc results folder, and identify which command/tool reported the error.
3. Locate the log of that particular command/tool within the module folder.

Index file is older than the data file error

This is typically caused by copy-pasting Resources files without preserving timestamps.
When moving/transfering files from one location to another, please make sure to preserve timestamps of Resources files.
Some of the tools check if index files are correct and may otherwise return an error.
We suggest using rsync -aP command to transfer files. Alternatively, consider transfering the NeoDisc.tar.gz and extract the Resources folder to ensure maintaining timestamps

R / Python library not found

It is typically caused by singularity loading local home and environment within the container, which may interfer with those in the container.
Try adding options --cleanenv --no-home to the singularity command in NeoDisc.sh wrapper script:

singularity exec --cleanenv --no-home -B ${bindpath} ${containerpath}/NeoDisc.sif ${neodisc_arguments}

ERROR: GERMLINE WES/WGS ALIGNMENT FAILED:

• Check the path to the WES/WGS fastq files in the configuration file.
• Check the formatting of the WES/WGS fastq filenames and make sure it is correct and fits with the -t and -g arguments provided.

ERROR: HLA-TYPING ANALYSIS FAILED

• Check the path to the WES/WGS and RNAseq fastq files in the configuration file
• Check the formatting of the WES/WGS and RNAseq fastq filenames and make sure it is correct and fits with the -t, -g, and -rna arguments provided.
• Make sure that you have paired-end sequencing WES/WGS and RNAseq files

ERROR: RNA sample RNASEQ ANALYSIS FAILED

• Check the path to the RNAseq fastq files in the configuration file
• Check the formatting of the RNAseq fastq fileames and make sure it is correct and fits with the -rna argument(s) provided.

ERROR: MS SPECTRA CONVERSION FAILED

• Check the path to the MS files in the configuration file
• Sometimes MS conversion may fail. Try re-running NeoDisc and see if the issue is solved.

Restarting a failed analysis

If you ran your analysis in fastq mode, use the -resume option

Rerun a specific module

1. Delete the module output folder
2. use the -resume option