Failed to pull singularity image viroprofiler-base:v0.2.2, manifest unknown

liuronghyw commented 1 year ago

Description of the bug

Dear Dr. Long, I have tried to install viroprofile for about two weeks, but still failed. When I install the newest version of viroprofiler with the following command: nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup" --db "/public/home/hpc4011032/db/viroprofiler"

The error:

N E X T F L O W ~ version 22.10.6 WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config Launching https://github.com/deng-lab/viroprofiler [infallible_khorana] DSL2 - revision: 222364d5b7 [main]

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`888' 888 888 888 888 // || \\ 888 888 888 888 888 888 888 .o 888` 8' o888o d888b `Y8bod8P' // \\ d888b`Y8bod8P' o888o o888o o888o `Y8bod8P' d888b ViroProfiler v0.2

Core Nextflow options revision : main runName : infallible_khorana containerEngine: singularity launchDir : /public/home/hpc4011032/ICB_viro/viroprofiler workDir : /public/home/hpc4011032/ICB_viro/viroprofiler/work projectDir : /public/home/hpc4011032/.nextflow/assets/deng-lab/viroprofiler userName : hpc4011032 profile : singularity configFiles : /public/home/hpc4011032/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options mode : setup db : /public/home/hpc4011032/db/viroprofiler outdir : output

Others use_iphop : true use_dram : true

Max job request options max_cpus : 1 max_memory : 8.GB max_time : 12.h

!! Only displaying parameters that differ from the pipeline defaults !!

If you use ViroProfiler for your analysis please cite:

The ViroProfiler pipeline https://doi.org/10.1080/19490976.2023.2192522
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md

[- ] process > VIROPROFILER:SETUP:DB_CHECKV - [- ] process > VIROPROFILER:SETUP:DB_VIBRANT [ 0%] 0 of 1 executor > local (3) [- ] process > VIROPROFILER:SETUP:DB_CHECKV - executor > local (3) [- ] process > VIROPROFILER:SETUP:DB_CHECKV - executor > local (3) [- ] process > VIROPROFILER:SETUP:DB_CHECKV - executor > local (3) [- ] process > VIROPROFILER:SETUP:DB_CHECKV - [ec/d12e50] process > VIROPROFILER:SETUP:DB_VIBRANT [100%] 1 of 1 ✔ [- ] process > VIROPROFILER:SETUP:DB_VIRSORTER2 - [61/71fda0] process > VIROPROFILER:SETUP:DB_DRAM [100%] 1 of 1 ✔ [b1/56b5ad] process > VIROPROFILER:SETUP:DB_IPHOP [100%] 1 of 1 ✔ executor > local (3) [- ] process > VIROPROFILER:SETUP:DB_CHECKV - [ec/d12e50] process > VIROPROFILER:SETUP:DB_VIBRANT [100%] 1 of 1 ✔ [- ] process > VIROPROFILER:SETUP:DB_VIRSORTER2 - [61/71fda0] process > VIROPROFILER:SETUP:DB_DRAM [100%] 1 of 1 ✔ [b1/56b5ad] process > VIROPROFILER:SETUP:DB_IPHOP [100%] 1 of 1 ✔ [- ] process > VIROPROFILER:SETUP:DB_VREFSEQ - Pulling Singularity image docker://denglab/viroprofiler-base:v0.2.2 [cache /public/home/hpc4011032/ICB_viro/viroprofiler/./temp/denglab-viroprofiler-base-v0.2.2.img] Pulling Singularity image docker://denglab/viroprofiler-base:v0.2 [cache /public/home/hpc4011032/ICB_viro/viroprofiler/./temp/denglab-viroprofiler-base-v0.2.img] Error executing process > 'VIROPROFILER:SETUP:DB_VIRSORTER2'

Caused by: Failed to pull singularity image command: singularity pull --name denglab-viroprofiler-base-v0.2.2.img.pulling.1682469314842 docker://denglab/viroprofiler-base:v0.2.2 > /dev/null status : 255 message: FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://denglab/viroprofiler-base:v0.2.2: Error reading manifest v0.2.2 in docker.io/denglab/viroprofiler-base: manifest unknown: manifest unknown

Would you please help me about this issue ?

Command used and terminal output

nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup" --db "/public/home/hpc4011032/db/viroprofiler"

Relevant files

报错信息

System information

N E X T F L O W ~ version 22.10.6

HPC

slurm

Singularity

CentOS Linux

viroprofiler 0.2.2

XC-Zhai commented 1 year ago

I had the same issue, you can run: nextflow run deng-lab/viroprofiler -r fix_iphop -profile singularity --mode "setup" , would set up most steps.

Best, Xichuan

rujinlong commented 1 year ago

This bug is fixed in v0.2.3. Please update the pipeline using nextflow pull deng-lab/viroprofiler and rerun using parameter -r main or -r v0.2.3.

deng-lab / viroprofiler