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nanoporetech / isONclust2

A tool for de novo clustering of long transcriptomic reads
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Cluster Errors #3

Closed ErisonChen closed 4 years ago

ErisonChen commented 4 years ago

hi ,sir When we used the commands isONclust2 cluster -v -l isONclust2_batches/batches/isONbatch_0.cer -o b0.cer,the following errors appeared.And the output file b0.cer did not exist.

    Batch number: 0
    Batch range: [0,24669]
    Depth: -1
    Nr sequences: 24670
    Nr bases: 50001410
    Nr clusters: 24670
    Nr nontrivial clusters: 0
    Minimizers in database: 0
Created pseudo-batch for single clustering:
    Batch number: 0
    Batch range: [0,24669]
    Depth: -1
    Nr sequences: 24670
    Nr bases: 0
    Nr clusters: 24670
    Nr nontrivial clusters: 0
    Minimizers in database: 0
Resetting input clusters.
Clustering mode: Invalid clustering mode: 3

Then ,we added -x furious to this command isONclust2 cluster -x furious -l isONclust2_batches/batches/isONbatch_0.cer -o b0.cer. It worked.

Please help us telling that is a error or not .And how did it come out .

splaisan commented 4 years ago

conda install: isONclust2 version: v2.3-e9da596

isONclust2 sort -B 10000 -v reads.fq

# I get 18 batches
-rw-rw-r-- 1 user user 440M Oct 24 18:12 isONbatch_0.cer
-rw-rw-r-- 1 user user 447M Oct 24 18:12 isONbatch_1.cer
-rw-rw-r-- 1 user user 353M Oct 24 18:12 isONbatch_2.cer
-rw-rw-r-- 1 user user 249M Oct 24 18:12 isONbatch_3.cer
-rw-rw-r-- 1 user user  98M Oct 24 18:12 isONbatch_4.cer
...
-rw-rw-r-- 1 user user  98M Oct 24 18:12 isONbatch_17.cer

# then try to merge them
isONclust2 cluster -v -l isONbatch_0.cer -r isONbatch_1.cer -o b0_1.cer
Loaded input batch from isONbatch_0.cer:
    Batch number: 0
    Batch range: [0,2762]
    Depth: -1
    Nr sequences: 2763
    Nr bases: 10002043
    Nr clusters: 2763
    Nr nontrivial clusters: 0
    Minimizers in database: 0
Loaded input batch from isONbatch_1.cer:
    Batch number: 1
    Batch range: [2763,5850]
    Depth: -1
    Nr sequences: 3088
    Nr bases: 10000834
    Nr clusters: 3088
    Nr nontrivial clusters: 0
    Minimizers in database: 0
Clustering mode: Invalid clustering mode: 3

with extra -x option `-x fast` or `-x furious` or `-x sahlin` I get `Segmentation fault (core dumped) ` after some runtime
# packages in environment at /opt/miniconda3/envs/isonclust2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_tflow_select             2.3.0                       mkl  
absl-py                   0.10.0                   py36_0  
astor                     0.8.1                    py36_0  
bcftools                  1.9                  ha228f0b_4    bioconda
biopython                 1.78             py36h7b6447c_0  
blas                      1.0                         mkl  
bz2file                   0.98                     py36_1  
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.16.1               h7b6447c_0  
ca-certificates           2020.10.14                    0  
certifi                   2020.6.20                py36_0  
cffi                      1.14.0           py36h2e261b9_0  
curl                      7.69.1               hbc83047_0  
decorator                 4.4.2                      py_0  
gast                      0.4.0                      py_0  
google-pasta              0.2.0                      py_0  
grpcio                    1.31.0           py36hf8bcb03_0  
h5py                      2.7.1            py36ha1f6525_2  
hdf5                      1.10.2               hba1933b_1  
htslib                    1.9                  ha228f0b_7    bioconda
importlib-metadata        2.0.0                      py_1  
intel-openmp              2020.2                      254  
intervaltree              3.1.0                      py_0  
isonclust2                2.3                  hc9558a2_0    bioconda
k8                        0.2.5                he513fc3_0    bioconda
keras-applications        1.0.8                      py_1  
keras-preprocessing       1.1.0                      py_1  
krb5                      1.17.1               h173b8e3_0  
ld_impl_linux-64          2.33.1               h53a641e_7  
libcurl                   7.69.1               h20c2e04_0  
libdeflate                1.0                  h14c3975_1    bioconda
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1             hf484d3e_1007  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
libprotobuf               3.13.0.1             hd408876_0  
libssh2                   1.9.0                h1ba5d50_1  
libstdcxx-ng              9.1.0                hdf63c60_0  
mappy                     2.17             py36h84994c4_0    bioconda
markdown                  3.3.2                    py36_0  
medaka                    0.11.5           py36h148d290_0    bioconda
minimap2                  2.17                 hed695b0_3    bioconda
mkl                       2020.2                      256  
mkl-service               2.3.0            py36he904b0f_0  
mkl_fft                   1.2.0            py36h23d657b_0  
mkl_random                1.1.1            py36h0573a6f_0  
ncurses                   6.1                  he6710b0_1  
networkx                  2.5                        py_0  
numpy                     1.16.1           py36h7e9f1db_1  
numpy-base                1.16.1           py36hde5b4d6_1  
ont-fast5-api             1.0.1                      py_0    bioconda
openssl                   1.1.1h               h7b6447c_0  
parasail-python           1.2              py36h8b12597_0    bioconda
pip                       20.2.4                   py36_0  
protobuf                  3.13.0.1         py36he6710b0_1  
pycparser                 2.20                       py_2  
pyfaidx                   0.5.9.1            pyh864c0ab_1    bioconda
pysam                     0.15.3           py36hda2845c_1    bioconda
python                    3.6.10               h0371630_0  
pyvcf                     0.6.8                    py36_0    bioconda
readline                  7.0                  h7b6447c_5  
samtools                  1.9                 h10a08f8_12    bioconda
scipy                     1.5.2            py36h0b6359f_0  
setuptools                50.3.0           py36hb0f4dca_1  
six                       1.15.0                     py_0  
sortedcontainers          2.2.2                      py_0  
sqlite                    3.31.1               h7b6447c_0  
tensorboard               1.14.0           py36hf484d3e_0  
tensorflow                1.14.0          mkl_py36h2526735_0  
tensorflow-base           1.14.0          mkl_py36h7ce6ba3_0  
tensorflow-estimator      1.14.0                     py_0  
termcolor                 1.1.0                    py36_1  
tk                        8.6.10               hbc83047_0  
werkzeug                  1.0.1                      py_0  
whatshap                  0.18             py36h6bb024c_0    bioconda
wheel                     0.35.1                     py_0  
wrapt                     1.12.1           py36h7b6447c_1  
xopen                     0.7.3                      py_0    bioconda
xz                        5.2.5                h7b6447c_0  
zipp                      3.3.1                      py_0  
zlib                      1.2.11               h7b6447c_3
bsipos commented 4 years ago

Hi both, please do not use isONclust2 as a standalone program, rather as a part of the https://github.com/nanoporetech/pipeline-nanopore-denovo-isoforms pipeline.

splaisan commented 4 years ago

Thanks @bsipos, yes this is what I read elsewhere and stopped to use the app in standalone now.