---------------------------------------------------- ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' 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` #################################################### ## 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 https://github.com/nf-core/rnaseq