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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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There is no progression on the analysis/process #111

Open CurryMuthu opened 1 week ago

CurryMuthu commented 1 week ago

Operating System

Windows 10

Other Linux

No response

Workflow Version

v2.10.1

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Hi, its my first time using Epi2me to analyze about 40-60 fastq files. Is it normal for the process to take more than 12 hours?

Additionally, I have tried to download the Kraken2 Database as a Reference File (tar.gz) and its going to take more than a day to download. Any advice to this? Thank you!

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/mnt/c/Epi/workflows/epi2me-labs/wf-metagenomics/main.nf` [KrakenStandard8] DSL2 - revision: 6247543ce2
WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-metagenomics v2.10.1
--------------------------------------------------------------------------------
Core Nextflow options
  runName        : KrakenStandard8
  containerEngine: docker
  launchDir      : /mnt/c/Epi/instances/wf-metagenomics_01J1CDK9ZPNZ8260XVXQ9BDR6Q
  workDir        : /mnt/c/Epi/instances/wf-metagenomics_01J1CDK9ZPNZ8260XVXQ9BDR6Q/work
  projectDir     : /mnt/c/Epi/workflows/epi2me-labs/wf-metagenomics
  userName       : epi2mewsl
  profile        : standard
  configFiles    : /mnt/c/Epi/workflows/epi2me-labs/wf-metagenomics/nextflow.config
Input Options
  fastq          : /mnt/c/Users/CurryMuthu/Desktop/Nanopore Sequencing
Reference Options
  store_dir      : /mnt/c/Epi/data
  database_sets  : [ncbi_16s_18s:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_16s_18s.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ncbi_targeted_loci_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s/ref2taxid.targloci.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], ncbi_16s_18s_28s_ITS:[reference:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna, database:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS_kraken2.tar.gz, ref2taxid:https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2023-01-01.zip], SILVA_138_1:[database:null], Standard-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip], PlusPF-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_08gb_20230314.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip], PlusPFP-8:[database:https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_08gb_20230314.tar.gz, taxonomy:https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/new_taxdump_2023-03-01.zip]]
Output Options
  out_dir        : /mnt/c/Epi/instances/wf-metagenomics_01J1CDK9ZPNZ8260XVXQ9BDR6Q/output
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-metagenomics for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-metagenomics v2.10.1.
--------------------------------------------------------------------------------
Checking inputs.
Note: Memory available to the workflow must be slightly higher than size of the database Standard-8 index (8GB) or consider to use --kraken2_memory_mapping
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Note: Empty files or those files whose reads have been discarded after filtering based on read length and/or read quality will not appear in the report and will be excluded from subsequent analysis.
Kraken2 pipeline.
Preparing databases.
Using default taxonomy database.
Unpacking kraken2 indexes
[skipping] Stored process > prepare_databases:download_unpack_taxonomy
[b0/038b1e] Submitted process > fastcat (1)
[ea/6b2560] Submitted process > kraken_pipeline:run_common:getParams
[49/0ebcd2] Submitted process > prepare_databases:unpack_download_kraken2_database
[f4/08d263] Submitted process > kraken_pipeline:run_common:getVersions
[67/9dc6b5] Submitted process > kraken_pipeline:output_results (1)
[b6/d2f73e] Submitted process > kraken_pipeline:output_results (2)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

I have tried with the demo file and have at least ran for half a day and had no progression as well.
nggvs commented 6 days ago

Hi @CurryMuthu , The demo data should not take more than 10 minutes if the database is already downloaded (it is downloaded first time you run the workflow or the demo, but still should be less than half a day (although these times depends a little bit on the resources of the laptop, [requirements are in the README] and your internet connection). Could you try to run the demo of other pipeline to see if you also have the same problem of no progression, for example wf-alignment or wf-amplicon? Which is the version of the EPI2ME Desktop App? Are you running different analysis at the same time?