bounlu
commented
6 days ago When I use --no_charts flag for purple, it succeeds without generating the plots. However, this this time orange fails as the expected purple_plot_dir does not exist:
ERROR ~ Error executing process > 'NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE (220024755)'
Caused by:
Process `NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE (220024755)` terminated with an error exit status (1)
Command executed:
echo "5.34 [oncoanalyser]" > pipeline_version.txt
# When WTS data is present, ORANGE expects the somatic SAGE VCF to have appended WTS data; CS indicates this should
# occur after PURPLE. Since ORANGE only collects the somatic SAGE VCF from the PURPLE output directory, we must
# prepare accordingly
# Isofox inputs are also expected to have the tumor sample ID in the filename
# NOTES(SW): Use of symlinks was causing reliability issues on HPC with Singularity, switched to full file copy instead
purple_dir_local=purple
if [[ -n "" ]]; then
purple_dir_local=purple__prepared;
if [[ -d ${purple_dir_local}/ ]]; then
rm -r ${purple_dir_local}/;
fi
cp -rL purple ${purple_dir_local}/
cp -L ${purple_dir_local}/220024755.purple.somatic.vcf.gz;
if [[ -n "" ]]; then
cp -L ${purple_dir_local}/220024755.purple.germline.vcf.gz;
fi;
mkdir -p isofox_dir__prepared/;
for fp in /*; do
cp -L ${fp} isofox_dir__prepared/$(sed 's/null/220024755/' <<< ${fp##*/});
done;
fi
# Set input plot directory and create it doesn't exist. See the LINX visualiser module for further info.
if [[ ! -e plots/reportable/ ]]; then
mkdir -p plots/reportable/;
fi;
# NOTE(SW): '--add-opens java.base/java.time=ALL-UNNAMED' resolves issue writing JSON, see:
# https://stackoverflow.com/questions/70412805/what-does-this-error-mean-java-lang-reflect-inaccessibleobjectexception-unable/70878195#70878195
# NOTE(SW): DOID label: 162 [cancer]; Hartwig cohort group: unknown
mkdir -p output/
# NOTE(SW): manually locating ORANGE install directory so that we can applu `--add-opens`, won't fix old bioconda recipe
orange_bin_fp=$(which orange)
orange_install_dir=$(readlink ${orange_bin_fp} | xargs dirname)
orange_jar=$(dirname ${orange_bin_fp})/${orange_install_dir}/orange.jar
java \
--add-opens java.base/java.time=ALL-UNNAMED \
-Xmx6120328397 \
-jar ${orange_jar} \
\
\
-experiment_date $(date +%y%m%d) \
-add_disclaimer \
-pipeline_version_file pipeline_version.txt \
\
-tumor_sample_id 220024755 \
-primary_tumor_doids 162 \
-tumor_sample_wgs_metrics_file 220024755.wgsmetrics \
-tumor_sample_flagstat_file 220024755.flagstat \
-sage_dir somatic \
-purple_dir ${purple_dir_local} \
-purple_plot_dir ${purple_dir_local}/plot/ \
-linx_dir linx_somatic \
-linx_plot_dir plots/reportable/ \
-lilac_dir lilac \
\
\
\
\
\
\
\
\
\
\
\
\
\
\
-ref_genome_version 38 \
-doid_json doid.json \
-cohort_mapping_tsv cohort_mapping.tsv \
-cohort_percentiles_tsv cohort_percentiles.tsv \
-known_fusion_file known_fusion_data.38.csv \
-driver_gene_panel DriverGenePanel.tso500.38.tsv \
-ensembl_data_dir ensembl_data \
\
\
-output_dir output/
cat <<-END_VERSIONS > versions.yml
"NFCORE_ONCOANALYSER:TARGETED:ORANGE_REPORTING:ORANGE":
orange: $(orange -version | sed 's/^.* //')
END_VERSIONS
Command exit status:
1
Command output:
09:21:47 - [ERROR] - invalid path for config: purple_plot_dir = purple/plot/
Purplefails with the below error:Command used and terminal output
No response
Relevant files
No response
System information
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