qbic-pipelines / cellranger Goto Github PK

cellranger task was getting killed, changed to label high_process and completed. I suspect the default mem (7GB) is set too low with label cellranger. In my analysis, it peaked at 46GB.

when running:

nextflow run qbic-pipelines/cellranger

I'm getting:

N E X T F L O W ~ version 21.04.1
Launching cellranger/main.nf [lonely_turing] - revision: 04c22e90bc

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
qbic-pipelines/cellranger v1.0.1

Core Nextflow options
runName : lonely_turing
containerEngine : docker
container : qbicpipelines/cellranger:1.0
launchDir : /home/ec2-user/environment/qbic
workDir : /home/ec2-user/environment/qbic/work
projectDir : /home/ec2-user/environment/qbic/cellranger
userName : ec2-user
profile : test,docker
configFiles : /home/ec2-user/environment/qbic/cellranger/nextflow.config

Input/output options
input : https://raw.githubusercontent.com/qbic-pipelines/cellranger/master/testdata/input_data.tsv
index_file : true

Reference genome options
save_reference : false
reference_name : Homo_sapiens.GRCh38.chr_22
fasta : https://raw.githubusercontent.com/qbic-pipelines/cellranger/dev/testdata/Homo_sapiens.GRCh38.dna.chromosome.22.fa
gtf : https://raw.githubusercontent.com/qbic-pipelines/cellranger/dev/testdata/Homo_sapiens.GRCh38.104.chr_22.gtf

Generic options
max_multiqc_email_size : 25 MB

Max job request options
max_cpus : 2
max_memory : 6 GB
max_time : 2d

Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function

Only displaying parameters that differ from defaults.

[- ] process > get_software_versions -
[- ] process > get_references -
[- ] process > get_software_versions -
[- ] process > get_references -
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > get_references -
executor > local (1)
[- ] process > get_software_versions [ 0%] 0 of 1
executor > local (1)
[- ] process > get_software_versions [ 0%] 0 of 1
executor > local (2)
[da/985c31] process > get_software_versions [ 0%] 0 of 1
executor > local (3)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
executor > local (3)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
executor > local (4)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > get_references -
[ac/4eafc5] process > build_references (build_references) [100%] 1 of 1 ✔
executor > local (4)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > get_references -
[ac/4eafc5] process > build_references (build_references) [100%] 1 of 1 ✔
executor > local (5)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > get_references -
[ac/4eafc5] process > build_references (build_references) [100%] 1 of 1 ✔
executor > local (5)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > get_references -
[ac/4eafc5] process > build_references (build_references) [100%] 1 of 1 ✔
executor > local (6)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > get_references -
[ac/4eafc5] process > build_references (build_references) [100%] 1 of 1 ✔
executor > local (6)
[da/985c31] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > get_references -
[ac/4eafc5] process > build_references (build_references) [100%] 1 of 1 ✔
[8a/3afba2] process > fastqc (pbmc_1k_v3_mini) [100%] 2 of 2 ✔[dd/2baeeb] process > count (Library1) [ 0%] 0 of 1[- ] process > multiqc [ 0%] 0 of 1[5f/1aba8d] process > output_documentation [100%] 1 of 1 ✔WARN: Input tuple does not match input set cardinality declared by process count -- offending value: [Library1, [pbmc_1k_v3_mini, pbmc_1k_v3_mini], [L001, L002], [/qbic-pipelines/cellranger/master/testdata/pbmc_1k_v3_mini_S1_L001_R1_001.fastq.gz, /qbic-pipelines/cellranger/master/testdata/pbmc_1k_v3_mini_S1_L002_R1_001.fastq.gz], [/qbic-pipelines/cellranger/master/testdata/pbmc_1k_v3_mini_S1_L001_R2_001.fastq.gz, /qbic-pipelines/cellranger/master/testdata/pbmc_1k_v3_mini_S1_L002_R2_001.fastq.gz], [/qbic-pipelines/cellranger/master/testdata/pbmc_1k_v3_mini_S1_L001_I1_001.fastq.gz, /qbic-pipelines/cellranger/master/testdata/pbmc_1k_v3_mini_S1_L002_I1_001.fastq.gz]]