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nf-core / hlatyping

Precision HLA typing from next-generation sequencing data
https://nf-co.re/hlatyping
MIT License
63 stars 30 forks source link

Erorr running hlatyping with singularity #88

Closed nvk747 closed 4 years ago

nvk747 commented 4 years ago

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 ?

apeltzer commented 4 years ago

bash: singularity: command not found

You need to install singularity first ;-)

nvk747 commented 4 years ago

Ohh i Thought it installs automatically if that is the case I will close the issue thanks for the suggestion @apeltzer