Erorr running hlatyping with singularity
nvk747 opened this issue · 2 comments
I am currently using Conda for next flow with following version:
Version: 20.04.1 build 5335
Created: 03-05-2020 19:37 UTC (15:37 EDT)
System: Mac OS X 10.14.6
Runtime: Groovy 2.5.8 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS
Encoding: UTF-8 (UTF-8)
When I run this command :
(nextflow) lri-108040:hlatyping nagampv$ nextflow run ../hlatyping --input "/Users/nagampv/Desktop/nagampv_projects/SRR1200850_2_out.fastq.bam" --bam -profile singularity --outdir $PWD/test_results2
I am getting this error shown below.
Container : singularity - nfcore/hlatyping:1.1.5
Launch dir : /Users/nagampv/Desktop/nagampv_projects/hlatyping
Script dir : /Users/nagampv/Desktop/nagampv_projects/hlatyping
User : nagampv
Config Profile : singularity
[2m----------------------------------------------------
BAM file format detected. Initiate remapping to HLA alleles with yara mapper.
[- ] process > remap_to_hla -
[- ] process > remap_to_hla -
[- ] process > remap_to_hla -
[- ] process > make_ot_config -
[- ] process > run_optitype -
[- ] process > output_documentation -
[- ] process > get_software_versions -
[- ] process > multiqc -
Pulling Singularity image docker://nfcore/hlatyping:1.1.5 [cache /Users/nagampv/Desktop/nagampv_projects/hlatyping/work/singularity/nfcore-hlatyping-1.1.5.img]
[0;35m[nf-core/hlatyping] Pipeline completed with errors
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /Users/nagampv/Desktop/nagampv_projects/hlatyping/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'make_ot_config'
Caused by:
Failed to pull singularity image
command: singularity pull --name nfcore-hlatyping-1.1.5.img docker://nfcore/hlatyping:1.1.5 > /dev/null
status : 127
message:
bash: singularity: command not found
Appears like my command cannot pull singularity image. The same command works well with -profile docker
any suggestions ?
bash: singularity: command not found
You need to install singularity first ;-)