The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:
Error executing process > 'multiqc'
Caused by:
Process exceeded running time limit (4h)
Command executed:
multiqc . -f --config multiqc_config.yaml \
-m custom_content -m picard -m preseq -m rseqc -m featureCounts -m hisat2 -m star -m cutadapt -m sortmerna -m fastqc -m qualimap -m salmon
Command exit status:
-
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
/opt/conda/envs/nf-core-rnaseq-1.4.2/lib/python3.6/site-packages/multiqc/utils/config.py:45: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
configs = yaml.load(f)
/opt/conda/envs/nf-core-rnaseq-1.4.2/lib/python3.6/site-packages/multiqc/utils/config.py:51: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
sp = yaml.load(f)
/opt/conda/envs/nf-core-rnaseq-1.4.2/lib/python3.6/site-packages/multiqc/utils/config.py:121: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
new_config = yaml.load(f)
[WARNING] multiqc : MultiQC Version v1.9 now available!
[INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
[INFO ] multiqc : Only using modules custom_content, picard, preseq, rseqc, featureCounts, hisat2, star, cutadapt, sortmerna, fastqc, qualimap, salmon
/opt/conda/envs/nf-core-rnaseq-1.4.2/lib/python3.6/site-packages/multiqc/modules/custom_content/custom_content.py:84: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
parsed_data = yaml.load(f['f'])
/opt/conda/envs/nf-core-rnaseq-1.4.2/lib/python3.6/site-packages/multiqc/modules/custom_content/custom_content.py:321: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
hconfig = yaml.load("\n".join(hlines))
[INFO ] custom_content : nf-core-rnaseq-summary: Found 1 sample (html)
[INFO ] custom_content : nf-core-rnaseq-summary: Found 1525 samples (html)
[INFO ] custom_content : software_versions: Found 1 sample (html)
[INFO ] custom_content : software_versions: Found 1055 samples (html)
Work dir:
/home/srlab/Documents/Shelly/Ssalar/work/ba/2c84b5d124f9788c108a15e7aa9ef6
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
nextflow run nf-core/rnaseq -profile docker --reads '*_{1,2}.fastq.gz' --aligner hisat2 --max_memory 45.GB --fasta GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_genomic.fa --gtf GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_genomic.FIXED.gtf --fc_group_features_type gene_id --saveReference --saveTrimmed --saveUnaligned --saveAlignedIntermediatesefd50c97fd77bdc6b6161e3ee76f7ddd26c37302-b4e8-4a6f-aedc-953212042ce8https://github.com/nf-core/rnaseq.git, revision master (commit hash 3b6df9bd104927298fcdf69e97cca7ff1f80527c)These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.