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Error occurred during initialization of VM java/lang/NoClassDefFoundError: java/lang/Object #164

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moldach opened this issue Aug 26, 2020 · 2 comments
Open

Error occurred during initialization of VM java/lang/NoClassDefFoundError: java/lang/Object #164

moldach opened this issue Aug 26, 2020 · 2 comments
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bug Something isn't working

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@moldach
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moldach commented Aug 26, 2020 •
edited
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Snakemake version

5.8.1

NOTE: I will go over why I'm not using the latest version in the additional context section

Wrapper version

0.64.0/bio/fastqc

Describe the bug

I'm getting the following error trying to use the fastqc wrapper:

Error occurred during initialization of VM

Logs

Building DAG of jobs...
Using shell: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       qc_before_trim_r2
        1

[Wed Aug 26 09:34:45 2020]
Job 0: --- Quality check of raw data with FastQC before trimming.

python /scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/.snakemake/scripts/tmpb0_czsv2.wrapper.py
Activating conda environment: /scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/.snakemake/conda/91998b6c
fastqc  --quiet -t 1 --outdir /tmp/tmpjnd9fio7 /home/moldach/projects/def-mtarailo/common/WGS_6/MTG324/MTG324_R2.fastq.gz ' 2> logs/fastqc/MTG324_R2.log'
Error occurred during initialization of VM
java/lang/NoClassDefFoundError: java/lang/Object
Traceback (most recent call last):
  File "/scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/.snakemake/scripts/tmpb0_czsv2.wrapper.py", line 35, in <module>
    shell(
  File "/home/moldach/bin/snakemake/lib/python3.8/site-packages/snakemake/shell.py", line 156, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail;  fastqc  --quiet -t 1 --outdir /tmp/tmpjnd9fio7 /home/moldach/projects/def-mtarailo/common/WGS_6/MTG324/MTG324_R2.fastq.gz ' 2> logs$
[Wed Aug 26 09:35:09 2020]
Error in rule qc_before_trim_r2:
    jobid: 0
    output: qc/fastQC/before_trim/MTG324_R2_fastqc.html, qc/fastQC/before_trim/MTG324_R2_fastqc.zip
    log: logs/fastqc/MTG324_R2.log (check log file(s) for error message)
    conda-env: /scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/.snakemake/conda/91998b6c

RuleException:
CalledProcessError in line 140 of /scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/Snakefile:
Command 'source /home/moldach/miniconda3/bin/activate '/scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/.snakemake/conda/91998b6c'; set -euo pipefail;  python /scratch/moldach/MADDOG/V$
  File "/scratch/moldach/MADDOG/VCF-FILES/biostars439754/MTG353/Snakefile", line 140, in __rule_qc_before_trim_r2
  File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.8.0/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Minimal example

The config.yaml

# Files
REF_GENOME: "c_elegans.PRJNA13758.WS265.genomic.fa"
GENOME_ANNOTATION: "c_elegans.PRJNA13758.WS265.annotations.gff3"

# Tools
QC_TOOL: "fastQC"
TRIM_TOOL: "trimmomatic"
ALIGN_TOOL: "bwa"
MARKDUP_TOOL: "picard"
CALLING_TOOL: "varscan"
ANNOT_TOOL: "vep"

The Snakefile

# Directories------------------------------------------------------------------
configfile: "config.yaml"

# Setting the names of all directories
dir_list = ["REF_DIR", "LOG_DIR", "BENCHMARK_DIR", "QC_DIR", "TRIM_DIR", "ALIGN_DIR", "MARKDUP_DIR", "CALLING_DIR", "ANNOT_DIR"]
dir_names = ["refs", "logs", "benchmarks", "qc", "trimming", "alignment", "mark_duplicates", "variant_calling", "annotation"]
dirs_dict = dict(zip(dir_list, dir_names))

import os
import pandas as pd
# getting the samples information (names, path to r1 & r2) from samples.txt
samples_information = pd.read_csv("samples.txt", sep='\t', index_col=False)
# get a list of the sample names
sample_names = list(samples_information['sample'])
sample_locations = list(samples_information['location'])
samples_dict = dict(zip(sample_names, sample_locations))
# get number of samples
len_samples = len(sample_names)


# Rules -----------------------------------------------------------------------

rule all:
    input:
        expand('{QC_DIR}/{QC_TOOL}/before_trim/{sample}_{pair}_fastqc.{ext}', QC_DIR=dirs_dict["QC_DIR"], QC_TOOL=config["QC_TOOL"], sample=sample_names, pair=['R1', 'R2'], ext=['html', 'zip'])
		
		
def getHome(sample):
  return(list(os.path.join(samples_dict[sample],"{0}_{1}.fastq.gz".format(sample,pair)) for pair in ['R1','R2']))

rule qc_before_trim_r1:
    input:
        r1 = lambda wildcards: getHome(wildcards.sample)[0]
    output:
        html=os.path.join(dirs_dict["QC_DIR"],config["QC_TOOL"],"before_trim","{sample}_R1_fastqc.html"),
        zip=os.path.join(dirs_dict["QC_DIR"],config["QC_TOOL"],"before_trim","{sample}_R1_fastqc.zip"),
    params: ""
    log:
        "logs/fastqc/{sample}_R1.log"
    resources:
        mem = 1000,
        time = 30
    threads: 1
    message: """--- Quality check of raw data with FastQC before trimming."""
    wrapper:
        "0.64.0/bio/fastqc"

rule qc_before_trim_r2:
    input:
        r1 = lambda wildcards: getHome(wildcards.sample)[1]
    output:
        html=os.path.join(dirs_dict["QC_DIR"],config["QC_TOOL"],"before_trim","{sample}_R2_fastqc.html"),
        zip=os.path.join(dirs_dict["QC_DIR"],config["QC_TOOL"],"before_trim","{sample}_R2_fastqc.zip"),
    params: ""
    log:
        "logs/fastqc/{sample}_R2.log"
    resources:
        mem = 1000,
        time = 30
    threads: 1
    message: """--- Quality check of raw data with FastQC before trimming."""
    wrapper:
        "0.64.0/bio/fastqc"

Additional context

It was mentioned in the preamble to this issue that I should I try the newest version of Snakemake. I downloaded the newest version via:

$ mamba create -c conda-forge -c bioconda -n snakemake snakemake
$ conda activate snakemake

But now when I try a dry-run I get a Segmentation fault

Using the older version of Snakemake (for comparison)

$ source ~/bin/snakemake/bin/activate
(snakemake) $ snakemake -n -r
Building DAG of jobs...
Job counts:
        count   jobs
        1       all
        1       qc_before_trim_r1
        1       qc_before_trim_r2
        3

[Wed Aug 26 10:28:41 2020]
Job 2: --- Quality check of raw data with FastQC before trimming.
Reason: Missing output files: qc/fastQC/before_trim/MTG324_R2_fastqc.html, qc/fastQC/before_trim/MTG324_R2_fastqc.zip

[Wed Aug 26 10:28:41 2020]
Job 1: --- Quality check of raw data with FastQC before trimming.
Reason: Missing output files: qc/fastQC/before_trim/MTG324_R1_fastqc.zip, qc/fastQC/before_trim/MTG324_R1_fastqc.html

[Wed Aug 26 10:28:41 2020]
localrule all:
    input: qc/fastQC/before_trim/MTG324_R1_fastqc.html, qc/fastQC/before_trim/MTG324_R1_fastqc.zip, qc/fastQC/before_trim/MTG324_R2_fastqc.html, qc/fastQC/before_trim/MTG324_R2_fastqc.zip
    jobid: 0
    reason: Input files updated by another job: qc/fastQC/before_trim/MTG324_R2_fastqc.html, qc/fastQC/before_trim/MTG324_R2_fastqc.zip, qc/fastQC/before_trim/MTG324_R1_fastqc.zip, qc/fastQC/before_trim/MTG324_R1_fastqc.html

Job counts:
        count   jobs
        1       all
        1       qc_before_trim_r1
        1       qc_before_trim_r2
        3
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

$ deactivate

Newest version of Snakemake

$ conda activate snakemake
$ conda --version
5.23.0
$ snakemake -n -r
Segmentation fault

I guess other pertinent information is that I'm on an academic HPC with a SLURM scheduler.

$ cat /etc/os-release

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

The issue I see with me using the newest Snakemake version is the following:

If I were to run an interactive job (to get more memory) (via salloc --time=1:0:0 --mem=1000) and then try to submit a job (which is a full pipeline consisting of many wrappers) (via bash -c "nohup snakemake --profile slurm --use-conda --jobs 500 &") it would only run jobs as long as the interactive job was set for.

As I understand it, Snakemake needs to be run from the head node - it submit jobs to the SLURM scheduler.

Is it possible that Snakemake version 5.23.0 is more memory intensive than 5.8.1? And if so does this preclude me from using it?
@moldach moldach added the bug Something isn't working label Aug 26, 2020
@moldach
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moldach commented Aug 27, 2020

I've used the verbose flag -r to get a more comprehensive log:

Building DAG of jobs...
Creating conda environment https:/github.com/snakemake/snakemake-wrappers/raw/0.64.0/bio/fastqc/environment.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /tmp/tmp1y8ge388.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
        exit_code = getattr(module, func_name)(args, parser)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 117, in execute
        result[installer_type] = installer.install(prefix, pkg_specs, args, env)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda_env/installers/conda.py", line 40, in install
        unlink_link_transaction.execute()
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 244, in execute
        self.verify()
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
        return f(*args, **kwds)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 231, in verify
        exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 590, in _verify
        for exc in self.verify_executor.map(UnlinkLinkTransaction._verify_individual_level,
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 525, in map
        yield func(thing)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 411, in _verify_individual_level
        error_result = axn.verify()
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/core/path_actions.py", line 418, in verify
        create_link(self.source_full_path, self.intermediate_path, LinkType.copy)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/gateways/disk/create.py", line 373, in create_link
        copy(src, dst)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/gateways/disk/create.py", line 310, in copy
        _do_copy(src, dst)
      File "/home/moldach/miniconda3/lib/python3.8/site-packages/conda/gateways/disk/create.py", line 324, in _do_copy
        copyfileobj(fsrc, fdst, buffer_size)
    OSError: [Errno 5] Input/output error

`$ /home/moldach/miniconda3/bin/conda-env create --file /scratch/moldach/MADDOG/VCF-FILES/biostars439754/.snakemake/conda/f288ba8b.yaml --prefix /scratch/moldach/MADDOG/VCF-FILES/biostars439754/.snakemake/conda/f288ba8b`

  environment variables:
             ACLOCAL_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/share/aclocal
                 CIO_TEST=<not set>
       CMAKE_LIBRARY_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/lib64
        CMAKE_PREFIX_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0
  CONDA_AUTO_UPDATE_CONDA=false
                CONDA_EXE=/home/moldach/miniconda3/bin/conda
         CONDA_PYTHON_EXE=/home/moldach/miniconda3/bin/python
               CONDA_ROOT=/home/moldach/miniconda3
              CONDA_SHLVL=0
                    CPATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
                          el2016.4/openmpi/2.1.1/include:/cvmfs/restricted.computecanada.ca/easy
                          build/software/2017/Core/ifort/2016.4.258/include:/cvmfs/restricted.co
                          mputecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/includ
                          e/fftw:/cvmfs/restricted.computecanada.ca/easybuild/software/2017/Core
                          /imkl/11.3.4.258/mkl/include
       CPLUS_INCLUDE_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/include
           CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
           C_INCLUDE_PATH=/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/include
      EASYBUILD_BUILDPATH=/tmp/moldach
          LD_LIBRARY_PATH=/opt/software/slurm/lib
             LIBRARY_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
                          el2016.4/openmpi/2.1.1/lib:/cvmfs/soft.computecanada.ca/easybuild/soft
                          ware/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/lin
                          ux/compiler/lib/intel64:/cvmfs/restricted.computecanada.ca/easybuild/s
                          oftware/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/
                          linux/compiler/lib/intel64:/cvmfs/soft.computecanada.ca/easybuild/soft
                          ware/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linux
                          /compiler/lib/intel64:/cvmfs/restricted.computecanada.ca/easybuild/sof
                          tware/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linu
                          x/compiler/lib/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profil
                          es/gcc-5.4.0/lib64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/g
                          cc-5.4.0/lib:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core
                          /imkl/11.3.4.258/mkl/lib/intel64:/cvmfs/restricted.computecanada.ca/ea
                          sybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64:/cvmfs/rest
                          ricted.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/l
                          ib/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib
        LMOD_PACKAGE_PATH=/cvmfs/soft.computecanada.ca/config/lmod/
                  MANPATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
                          el2016.4/openmpi/2.1.1/share/man:/cvmfs/restricted.computecanada.ca/ea
                          sybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries_20
                          16.4.258/linux/man/common:/cvmfs/restricted.computecanada.ca/easybuild
                          /software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/
                          linux/man/common:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc
                          -5.4.0/share/man:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.
                          09/share/man:/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/sh
                          are/man::/opt/puppetlabs/puppet/share/man
      MIC_LD_LIBRARY_PATH=/cvmfs/restricted.computecanada.ca/easybuild/software/2017/Core/imkl/1
                          1.3.4.258/mkl/lib/mic:/cvmfs/restricted.computecanada.ca/easybuild/sof
                          tware/2017/Core/imkl/11.3.4.258/lib/intel64_lin_mic
               MODULEPATH=/opt/software/modulefiles:/cvmfs/soft.computecanada.ca/easybuild/modul
                          es/2017/avx2/MPI/intel2016.4/openmpi2.1:/cvmfs/soft.computecanada.ca/e
                          asybuild/modules/2017/avx2/Compiler/intel2016.4:/home/moldach/.local/e
                          asybuild/modules/2017/Core:/cvmfs/soft.computecanada.ca/easybuild/modu
                          les/2017/Core:/cvmfs/soft.computecanada.ca/custom/modules
                     PATH=/home/moldach/bin/snakemake/bin:/home/moldach/nb_distribution/:/home/m
                          oldach/miniconda3/condabin:/home/moldach/projects/def-mtgraovac/moldac
                          h/bin:/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compil
                          er/intel2016.4/openmpi/2.1.1/bin:/cvmfs/restricted.computecanada.ca/ea
                          sybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries_20
                          16.4.258/linux/bin/intel64:/cvmfs/restricted.computecanada.ca/easybuil
                          d/software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258
                          /linux/bin/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/g
                          cc-5.4.0/bin:/cvmfs/restricted.computecanada.ca/easybuild/software/201
                          7/Core/imkl/11.3.4.258/mkl/bin:/cvmfs/restricted.computecanada.ca/easy
                          build/software/2017/Core/imkl/11.3.4.258/bin:/cvmfs/soft.computecanada
                          .ca/custom/bin/computecanada:/cvmfs/soft.computecanada.ca/easybuild/bi
                          n:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca
                          /nix/var/nix/profiles/16.09/bin:/cvmfs/soft.computecanada.ca/nix/var/n
                          ix/profiles/16.09/sbin:/opt/software/bin:/opt/software/slurm/bin:/usr/
                          local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/opt/
                          dell/srvadmin/bin
          PKG_CONFIG_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/int
                          el2016.4/openmpi/2.1.1/lib/pkgconfig:/cvmfs/soft.computecanada.ca/nix/
                          var/nix/profiles/16.09/lib/pkgconfig:/cvmfs/soft.computecanada.ca/nix/
                          var/nix/profiles/16.09/share/pkgconfig
               PYTHONPATH=/cvmfs/soft.computecanada.ca/custom/python/site-packages
       REQUESTS_CA_BUNDLE=<not set>
     RSNT_LD_LIBRARY_PATH=/opt/software/slurm/lib
            SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt
__LMOD_Priority_MODULEPATH=/opt/software/modulefiles:-10
__LMOD_REF_COUNT_MODULEPATH=/opt/software/modulefiles:1;/cvmfs/soft.computecanada.ca/easybuild/mod
                          ules/2017/avx2/MPI/intel2016.4/openmpi2.1:1;/cvmfs/soft.computecanada.
                          ca/easybuild/modules/2017/avx2/Compiler/intel2016.4:1;/home/moldach/.l
                          ocal/easybuild/modules/2017/Core:1;/cvmfs/soft.computecanada.ca/easybu
                          ild/modules/2017/Core:1;/cvmfs/soft.computecanada.ca/custom/modules:1

     active environment : None
            shell level : 0
       user config file : /home/moldach/.condarc
 populated config files : /home/moldach/.condarc
          conda version : 4.8.4
    conda-build version : not installed
         python version : 3.8.3.final.0
       virtual packages : __glibc=2.17
       base environment : /home/moldach/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/moldach/miniconda3/pkgs
                          /home/moldach/.conda/pkgs
       envs directories : /home/moldach/miniconda3/envs
                          /home/moldach/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.4 requests/2.23.0 CPython/3.8.3 Linux/3.10.0-1062.12.1.el7.x86_64 centos/7.7.1908 glibc/2.17
                UID:GID : 3019658:3019658
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

@ManavalanG
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Relevant issue: #191
Relevant stackoverflow question: https://stackoverflow.com/q/64000711/3998252

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