Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

gcpp failing #271

Closed
marcodelapierre opened this issue Mar 18, 2020 · 3 comments
Closed

gcpp failing #271

marcodelapierre opened this issue Mar 18, 2020 · 3 comments
Labels
Consensus

Comments

@marcodelapierre
Copy link

marcodelapierre commented Mar 18, 2020 •
edited

Operating system
Ubuntu 18.04

Package name
pb-assembly 0.0.8

Conda environment
Built a container on 18 March 2020 with the following Dockerfile:

FROM continuumio/miniconda3:4.8.2

RUN apt update && apt install -y psmisc

RUN conda install -y -c bioconda pb-assembly=0.0.8

Note that I had to build a container rather than use the biocontainer, as currently this one is missing the package psmisc, which provides the required tool pstree

Describe the bug
I try and run the sample pipeline you provide at https://github.com/PacificBiosciences/pb-assembly#example-data-set
The pipeline fails with an error.

Error message
Screen error:

[ERROR]Task Node(4-polish/quiver-run/000000F) failed with exit-code=1
[ERROR]Task Node(4-polish/quiver-run/000000F_001) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: {Node(4-polish/quiver-run/000000F_001), Node(4-polish/quiver-run/000000F)}
[ERROR]ready: set()
	submitted: set()
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
[ERROR]Error for run(target=clr, config_fn=fc_unzip.cfg, logging_config_fn=None)
Traceback (most recent call last):
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 195, in run
    run_logged(target, config_fn)
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 184, in run_logged
    unzip_all(config, unzip_config_fn)
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 27, in unzip_all
    tasks_unzip.run_workflow(wf, config, unzip_config_fn)
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/tasks/unzip.py", line 739, in run_workflow
    job_dict=config['job.step.unzip.quiver'],
  File "/opt/conda/lib/python3.7/site-packages/falcon_kit/pype.py", line 195, in gen_parallel_tasks
    wf.refreshTargets()
  File "/opt/conda/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
    self._refreshTargets(updateFreq, exitOnFailure)
  File "/opt/conda/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
    raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: {Node(4-polish/quiver-run/000000F_001), Node(4-polish/quiver-run/000000F)}
Traceback (most recent call last):
  File "/opt/conda/bin/fc_unzip.py", line 11, in <module>
    load_entry_point('falcon-unzip==1.3.7', 'console_scripts', 'fc_unzip.py')()
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/mains/start_unzip.py", line 33, in main
    unzip.run(**vars(args))
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 195, in run
    run_logged(target, config_fn)
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 184, in run_logged
    unzip_all(config, unzip_config_fn)
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/unzip.py", line 27, in unzip_all
    tasks_unzip.run_workflow(wf, config, unzip_config_fn)
  File "/opt/conda/lib/python3.7/site-packages/falcon_unzip/tasks/unzip.py", line 739, in run_workflow
    job_dict=config['job.step.unzip.quiver'],
  File "/opt/conda/lib/python3.7/site-packages/falcon_kit/pype.py", line 195, in gen_parallel_tasks
    wf.refreshTargets()
  File "/opt/conda/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
    self._refreshTargets(updateFreq, exitOnFailure)
  File "/opt/conda/lib/python3.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
    raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: {Node(4-polish/quiver-run/000000F_001), Node(4-polish/quiver-run/000000F)}

First error inside 4-polish/quiver-run/000000F/run-P8ee12899d659aa.bash.stderr:

gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j $nproc -r ../../../quiver-split/refs/000000F/ref.fasta aln-000000F.bam            -o ${fasta_fn},${fastq_fn},cns.vcf
+ gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j 1 -r ../../../quiver-split/refs/000000F/ref.fasta aln-000000F.bam -o cns.fasta,cns.fastq,cns.vcf
rc=$?
+ rc=1
if [[ $rc != 0 ]]; then
    if [[ $VC_IGNORE_ERROR != 1 ]]; then
        echo ERROR gcpp failed. Maybe no reads for this block?
        exit 1
    else
        echo WARNING gcpp failed. Maybe no reads for this block.
        # We expect gcpp to write files even on error, so we do not need to "touch" them.
    fi
fi
+ [[ 1 != 0 ]]
+ [[ 0 != 1 ]]
+ echo ERROR gcpp failed. Maybe no reads for this 'block?'
+ exit 1
touch quiver_done.exit
+ touch quiver_done.exit
WARNING:root:Call '/bin/bash user_script.sh' returned 256.

There's a similar error in 4-polish/quiver-run/000000F_001/run-P483c9b764f6a24.bash.stderr

To Reproduce
I followed the steps you provide in the example mentioned above. I have only edited the runtime commands to use the container I have built:

mkdir -p /data/work/falcon/docker
cd /data/work/falcon/docker

cat << EOF >Dockerfile
FROM continuumio/miniconda3:4.8.2

RUN apt update && apt install -y psmisc

RUN conda install -y -c bioconda pb-assembly=0.0.8
EOF

docker build -t mycontainer .

cd ..
mkdir test_pb_official
cd test_pb_official

git clone https://github.com/cdunn2001/git-sym.git
git clone https://github.com/pb-cdunn/FALCON-examples.git
cd FALCON-examples
../git-sym/git-sym update run/greg200k-sv2

cd run/greg200k-sv2
docker run -u $(id -u):$(id -g) -v /data/work:/data/work -w $(pwd) --rm  mycontainer fc_run fc_run.cfg
docker run -u $(id -u):$(id -g) -v /data/work:/data/work -w $(pwd) --rm  mycontainer fc_unzip.py fc_unzip.cfg

Expected behavior
As you state: "If everything was installed properly the test case will exit cleanly and you should find fasta files with a
size greater than 0 in the 4-polish/cns-output directory."
@pb-dseifert
Copy link
Contributor

pb-dseifert commented Jul 11, 2020 •
edited

Hi @marcodelapierre
thanks for reporting this. We'll have a look.

@pb-dseifert pb-dseifert changed the title gccp failing gcpp failing Jul 11, 2020
@AntoineHo
Copy link

Hello, I have exactly the same error on the same dataset. Any idea on how to solve this ?

Ubuntu 18.10

# packages in environment at /home/lege/anaconda3/envs/pbasm:           
#                                                                       
# Name                    Version                   Build  Channel      
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
aioeasywebdav             2.4.0                 py37_1000    conda-forge
aiohttp                   3.6.2            py37h516909a_0    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
async-timeout             3.0.1                   py_1000    conda-forge
attrs                     19.3.0                     py_0    conda-forge  
bamtools                  2.5.1                he513fc3_6    bioconda     
bax2bam                   0.0.9                h018d624_7    bioconda     
bcrypt                    3.1.7            py37h8f50634_1    conda-forge  
bedtools                  2.29.2               hc088bd4_0    bioconda     
blasr                     5.3.3                h018d624_2    bioconda     
blasr_libcpp              5.3.3                h018d624_1    bioconda     
boto3                     1.14.20            pyh9f0ad1d_0    conda-forge  
botocore                  1.17.20            pyh9f0ad1d_0    conda-forge  
brotlipy                  0.7.0           py37h8f50634_1000    conda-forge
bwa                       0.7.17               hed695b0_7    bioconda     
bzip2                     1.0.8                h516909a_2    conda-forge  
ca-certificates           2020.6.20            hecda079_0    conda-forge  
cachetools                4.1.1                      py_0    conda-forge  
cairo                     1.16.0            h3fc0475_1005    conda-forge  
certifi                   2020.6.20        py37hc8dfbb8_0    conda-forge  
cffi                      1.14.0           py37hd463f26_0    conda-forge  
chardet                   3.0.4           py37hc8dfbb8_1006    conda-forge
configargparse            1.2.3              pyh9f0ad1d_0    conda-forge  
crc32c                    2.0              py37h516909a_0    conda-forge  
cryptography              2.9.2            py37hb09aad4_0    conda-forge  
curl                      7.71.1               he644dc0_1    conda-forge  
datrie                    0.8.2            py37h8f50634_0    conda-forge  
decorator                 4.4.2                      py_0    conda-forge  
docutils                  0.15.2                   py37_0    conda-forge  
dropbox                   10.1.1             pyh9f0ad1d_0    conda-forge  
expat                     2.2.9                he1b5a44_2    conda-forge  
falcon-kit                1.8.1                    pypi_0    pypi         
falcon-phase              1.2.0                    pypi_0    pypi         
falcon-unzip              1.3.7                    pypi_0    pypi               
fftw                      3.3.8           mpi_mpich_h3f9e1be_1011    conda-forge
filechunkio               1.8                        py_2    conda-forge        
fontconfig                2.13.1            h1056068_1002    conda-forge        
freetype                  2.10.2               he06d7ca_0    conda-forge        
ftputil                   4.0.0                      py_0    conda-forge        
future                    0.18.2           py37hc8dfbb8_1    conda-forge        
gdk-pixbuf                2.36.12           h3f25603_1005    conda-forge        
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge        
ghostscript               9.22              hf484d3e_1001    conda-forge        
giflib                    5.1.7                h516909a_1    conda-forge        
gitdb                     4.0.5                      py_0    conda-forge        
gitpython                 3.1.3                      py_0    conda-forge        
glib                      2.65.0               h6f030ca_0    conda-forge        
gobject-introspection     1.64.1           py37h619baee_1    conda-forge        
google-api-core           1.17.0           py37hc8dfbb8_0    conda-forge        
google-api-python-client  1.9.1              pyh9f0ad1d_1    conda-forge        
google-auth               1.19.0                     py_0    conda-forge        
google-auth-httplib2      0.0.3                      py_3    conda-forge        
google-cloud-core         1.3.0                      py_0    conda-forge        
google-cloud-storage      1.28.1             pyh9f0ad1d_0    conda-forge        
google-resumable-media    0.5.1              pyh9f0ad1d_0    conda-forge        
googleapis-common-protos  1.51.0           py37hc8dfbb8_2    conda-forge        
graphite2                 1.3.13            he1b5a44_1001    conda-forge        
graphviz                  2.38.0            hf68f40c_1011    conda-forge        
harfbuzz                  2.4.0                hee91db6_5    conda-forge        
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge    
htslib                    1.9                  h4da6232_3    bioconda           
httplib2                  0.18.1             pyh9f0ad1d_0    conda-forge        
icu                       67.1                 he1b5a44_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
imagemagick               7.0.8_54        pl526h39023e4_0    conda-forge
importlib-metadata        1.7.0            py37hc8dfbb8_0    conda-forge
importlib_metadata        1.7.0                         0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jbig                      2.1               h516909a_2002    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
jmespath                  0.10.0             pyh9f0ad1d_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
jsonschema                3.2.0            py37hc8dfbb8_1    conda-forge
jupyter_core              4.6.3            py37hc8dfbb8_1    conda-forge
k8                        0.2.5                he513fc3_0    bioconda   
krb5                      1.17.1               hfafb76e_1    conda-forge
ld_impl_linux-64          2.34                 h53a641e_7    conda-forge
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcroco                  0.6.13               h8d621e5_1    conda-forge
libcurl                   7.71.1               hcdd3856_1    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         h46ee950_1    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.5.0                hdf63c60_6    conda-forge
libiconv                  1.15              h516909a_1006    conda-forge
liblapack                 3.8.0               17_openblas    conda-forge
libopenblas               0.3.10               h5ec1e0e_0    conda-forge
libpng                    1.6.37               hed695b0_1    conda-forge
libprotobuf               3.12.3               h8b12597_1    conda-forge
librsvg                   2.44.14              h11c8777_0    conda-forge
libssh2                   1.9.0                hab1572f_3    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libtool                   2.4.6             h14c3975_1002    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.0.2                hf4e8a37_4    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.10               h72b56ed_1    conda-forge
llvm-openmp               10.0.0               hc9558a2_0    conda-forge
lz4-c                     1.9.2                he1b5a44_1    conda-forge
markupsafe                1.1.1            py37h8f50634_1    conda-forge
minimap2                  2.17                 hed695b0_2    bioconda   
mpi                       1.0                       mpich    conda-forge
mpich                     3.3.2                hc856adb_0    conda-forge
multidict                 4.7.5            py37h8f50634_1    conda-forge
mummer4                   4.0.0beta2      pl526he1b5a44_5    bioconda   
nbformat                  5.0.7                      py_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
networkx                  2.4                        py_1    conda-forge
nim-falcon                1.5.1                h1341992_0    bioconda   
numpy                     1.18.5           py37h8960a57_0    conda-forge
oauth2client              4.1.3                      py_0    conda-forge
openjpeg                  2.3.1                h981e76c_3    conda-forge
openssl                   1.1.1g               h516909a_1    conda-forge
pandas                    1.0.5            py37h0da4684_0    conda-forge
pango                     1.40.14           he7ab937_1005    conda-forge
paramiko                  2.7.1                    py37_0    conda-forge
pb-assembly               0.0.8                         0    bioconda   
pb-dazzler                0.0.1                h516909a_0    bioconda   
pb-falcon                 2.2.4            py37hed50d52_0    bioconda      
pb-falcon-phase           0.1.0                h3889886_0    bioconda      
pbbam                     1.0.6                hc16d5b3_0    bioconda      
pbcopper                  1.3.0                h3e4de3e_0    bioconda      
pbgcpp                    1.9.0                         0    bioconda      
pbmm2                     1.3.0                h56fc30b_0    bioconda      
pcre                      8.44                 he1b5a44_0    conda-forge   
perl                      5.26.2            h516909a_1006    conda-forge   
pip                       20.1.1                     py_1    conda-forge   
pixman                    0.38.0            h516909a_1003    conda-forge   
pkg-config                0.29.2            h516909a_1006    conda-forge   
prettytable               0.7.2                      py_3    conda-forge   
protobuf                  3.12.3           py37h3340039_0    conda-forge   
psutil                    5.7.0            py37h8f50634_1    conda-forge   
pthread-stubs             0.4               h14c3975_1001    conda-forge   
pyasn1                    0.4.8                      py_0    conda-forge   
pyasn1-modules            0.2.7                      py_0    conda-forge   
pycparser                 2.20               pyh9f0ad1d_2    conda-forge   
pygments                  2.6.1                      py_0    conda-forge   
pygraphviz                1.5             py37h8f50634_1002    conda-forge 
pynacl                    1.3.0           py37h516909a_1001    conda-forge 
pyopenssl                 19.1.0                     py_1    conda-forge   
pyrsistent                0.16.0           py37h8f50634_0    conda-forge   
pysam                     0.16.0.1         py37hc334e0b_1    bioconda      
pysftp                    0.2.9                      py_1    conda-forge   
pysocks                   1.7.1            py37hc8dfbb8_1    conda-forge   
python                    3.7.6           cpython_h8356626_6    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge   
python-edlib              1.3.8.post1      py37h9a982cc_2    bioconda      
python-intervaltree       3.0.2                      py_0    bioconda      
python-irodsclient        0.8.2                      py_0    conda-forge  
python-msgpack            0.6.1            py37h9a982cc_3    bioconda     
python-sortedcontainers   2.2.2              pyh9f0ad1d_0    bioconda     
python_abi                3.7                     1_cp37m    conda-forge  
pytz                      2020.1             pyh9f0ad1d_0    conda-forge  
pyyaml                    5.3.1            py37h8f50634_0    conda-forge  
racon                     1.4.13               he513fc3_0    bioconda     
ratelimiter               1.2.0           py37hc8dfbb8_1001    conda-forge
readline                  8.0                  h46ee950_1    conda-forge  
requests                  2.24.0             pyh9f0ad1d_0    conda-forge  
rsa                       4.6                pyh9f0ad1d_0    conda-forge  
s3transfer                0.3.3            py37hc8dfbb8_1    conda-forge  
samtools                  1.9                 h10a08f8_12    bioconda     
setuptools                49.2.0           py37hc8dfbb8_0    conda-forge  
simplejson                3.17.0           py37h8f50634_1    conda-forge  
six                       1.15.0             pyh9f0ad1d_0    conda-forge  
slacker                   0.14.0                     py_0    conda-forge  
smmap                     3.0.4              pyh9f0ad1d_0    conda-forge  
snakemake                 5.20.1                        0    bioconda     
snakemake-minimal         5.20.1                     py_0    bioconda     
sqlite                    3.32.3               hcee41ef_1    conda-forge  
tk                        8.6.10               hed695b0_0    conda-forge  
toposort                  1.5                        py_3    conda-forge  
traitlets                 4.3.3            py37hc8dfbb8_1    conda-forge  
uritemplate               3.0.1                      py_0    conda-forge  
urllib3                   1.25.9                     py_0    conda-forge  
wheel                     0.34.2                     py_1    conda-forge  
wrapt                     1.12.1           py37h8f50634_1    conda-forge  
xmlrunner                 1.7.7                      py_0    conda-forge  
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge  
xorg-libice               1.0.10               h516909a_0    conda-forge  
xorg-libsm                1.2.3             h84519dc_1000    conda-forge  
xorg-libx11               1.6.9                h516909a_0    conda-forge  
xorg-libxau               1.0.9                h14c3975_0    conda-forge  
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge  
xorg-libxext              1.3.4                h516909a_0    conda-forge  
xorg-libxpm               3.5.13               h516909a_0    conda-forge  
xorg-libxrender           0.9.10            h516909a_1002    conda-forge  
xorg-libxt                1.1.5             h516909a_1003    conda-forge  
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge  
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge  
xorg-xproto               7.0.31            h14c3975_1007    conda-forge  
xz                        5.2.5                h516909a_1    conda-forge  
yaml                      0.2.5                h516909a_0    conda-forge  
yarl                      1.3.0           py37h516909a_1000    conda-forge
zipp                      3.1.0                      py_0    conda-forge  
zlib                      1.2.11            h516909a_1006    conda-forge  
zstd                      1.4.4                h6597ccf_3    conda-forge

File run-P3f542ff9b584b7.bash.stderr

set +e
+ set +e
gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j $nproc -r ../../../quiver-split/refs/000000F/ref.fasta aln-000000F.bam            -o ${fasta_fn},${fastq_fn},cns.vcf
+ gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j 1 -r ../../../quiver-split/refs/000000F/ref.fasta aln-000000F.bam -o cns.fasta,cns.fastq,cns.vcf
rc=$?
+ rc=1
if [[ $rc != 0 ]]; then
    if [[ $VC_IGNORE_ERROR != 1 ]]; then
        echo ERROR gcpp failed. Maybe no reads for this block?
        exit 1
    else
        echo WARNING gcpp failed. Maybe no reads for this block.
        # We expect gcpp to write files even on error, so we do not need to "touch" them.
    fi
fi
+ [[ 1 != 0 ]]
+ [[ 0 != 1 ]]
+ echo ERROR gcpp failed. Maybe no reads for this 'block?'
+ exit 1
touch quiver_done.exit
+ touch quiver_done.exit
WARNING:root:Call '/bin/bash user_script.sh' returned 256.
INFO:root:CD: 'uow-00' -> '/mnt/sda1/Antoine/22-06-20_HiCHomologs/TEST/pb-asm/FALCON-examples/run/greg200k-sv2/4-polish/quiver-run/000000F'
ERROR:root:failed multiprocessing
multiprocessing.pool.RemoteTraceback: 
...

I looked into the folder uow-00 and I cannot find the output of gcpp. I am guessing that it should contain these files: cns.fasta, cns.fastq, cns.vcf.

When I try to send manually the command found in run-P3f542ff9b584b7.bash.stderr, the shell is freed immediately without any error message but no output files either. It does not seem to run at all.

$ time gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j 1 -r ../../../quiver-split/refs/000000F/ref.fasta aln-000000F.bam -o cns.fasta,cns.fastq,cns.vcf
gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j 1 -r  aln-000000F.bam -o   0.00s user 0.00s system 93% cpu 0.006 total
$ ls
aln-000000F.bam  aln-000000F.bam.bai  aln-000000F.bam.pbi  quiver_done.exit  user_script.sh

Any idea how to solve this?

Cheers,
AH

@pb-cdunn
Copy link

First, because of changes in conda or bioconda, I needed this:

conda install samtools=1.9

Second, I think it works without pstree, except the error message at the end won't show the process-tree, so I don't think you need psmisc.

Third,

+ pbmm2 align --sort ../../../quiver-split/refs/000000F/ref.fasta /localdisk/scratch/cdunn/bioc/bioconda-recipes/recipes/pbipa/FALCON-examples/run/greg200k-sv2/4-polish/segregate-run/segr000/segregated/000000F/000000F.bam aln-000000F.bam
+ pbindex aln-000000F.bam
user_script.sh: line 22: pbindex: command not found

That means pbindex is missing. That is in pbbam, so simply run this:

conda install pbbam
which pbindex

But I guess you got through all those parts.

Finally, the bug.

+ gcpp --algorithm=arrow -x 5 -X 120 -q 0 -j 1 -r ../../../quiver-split/refs/000000F/ref.fasta     aln-000000F.bam -o cns.fasta,cns.fastq,cns.vcf
...
+ echo ERROR gcpp failed. Maybe no reads for this 'block?'

I've pushed a new tarball -- based on newer chemistry -- into pacbcloud. If you update FALCON-examples and re-run your git-sym command, you'll have it. You should then cd run/greg-200k-sv2; rm -rf 3-* 4-*; make unzip. Or just clean and re-run the whole thing. It works for me now.

@AntoineHo AntoineHo mentioned this issue Aug 27, 2020
Closed
@goeckeritz goeckeritz mentioned this issue Dec 29, 2020
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
Consensus
Milestone
No milestone
Development

No branches or pull requests
4 participants
@pb-cdunn @marcodelapierre @AntoineHo @pb-dseifert