nf-core/rnaseq v1.4.2
Run Name: jolly_meitner
nf-core/rnaseq execution completed unsuccessfully!
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`
The workflow was completed at 2020-11-04T19:37:30.969-08:00 (duration: 11h 42m 39s)
The command used to launch the workflow was as follows:
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 --saveAlignedIntermediates
Pipeline Configuration:
| Pipeline Release | master |
|---|---|
| Run Name | jolly_meitner |
| Reads | *_{1,2}.fastq.gz |
| Data Type | Paired-End |
| Strandedness | None |
| Trimming | 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0 |
| Aligner | HISAT2 |
| Fasta Ref | GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_genomic.fa |
| GTF Annotation | GCF_000233375.1_ICSASG_v2/GCF_000233375.1_ICSASG_v2_genomic.FIXED.gtf |
| Remove Ribosomal RNA | false |
| Biotype GTF field | gene_id |
| Save prefs | Ref Genome: Yes / Trimmed FastQ: Yes / Alignment intermediates: Yes |
| Max Resources | 45.GB memory, 16 cpus, 10d time per job |
| Container | docker - nfcore/rnaseq:1.4.2 |
| Output dir | ./results |
| Launch dir | /home/srlab/Documents/Shelly/Ssalar |
| Working dir | /home/srlab/Documents/Shelly/Ssalar/work |
| Script dir | /home/srlab/.nextflow/assets/nf-core/rnaseq |
| User | srlab |
| Config Profile | docker |
| Date Started | 2020-11-04T07:54:51.714-08:00 |
| Date Completed | 2020-11-04T19:37:30.969-08:00 |
| Pipeline script file path | /home/srlab/.nextflow/assets/nf-core/rnaseq/main.nf |
| Pipeline script hash ID | efd50c97fd77bdc6b6161e3ee76f7ddd |
| Pipeline repository Git URL | https://github.com/nf-core/rnaseq.git |
| Pipeline repository Git Commit | 3b6df9bd104927298fcdf69e97cca7ff1f80527c |
| Pipeline Git branch/tag | master |
| Docker image | nfcore/rnaseq:1.4.2 |
| Nextflow Version | 20.07.1 |
| Nextflow Build | 5412 |
| Nextflow Compile Timestamp | 24-07-2020 15:18 UTC |
nf-core/rnaseq