Take long time?

[YT123-coder]

Hi, I have been running concoct for contig file (ca. 500MB) for almost 3 days, but the log is stuck like below. Does concoct need considerable time for accomplishment? or Do I make mistakes?

The command I run from installation to activation is also written below

Best Regards,

log 2020-06-17 17:58:17,728:INFO:root:Results created at /Users/yuyatsukamoto/Desktop/metagenome/metagenome/Metagenome_Mizusawa_black/Raw_fastq_2/Concocut_output 2020-06-17 17:59:05,516:INFO:root:Successfully loaded composition data. 2020-06-17 17:59:06,242:INFO:root:Successfully loaded coverage data. 2020-06-17 17:59:07,469:INFO:root:Performed PCA, resulted in 54 dimensions 2020-06-17 17:59:20,015:INFO:root:Wrote original filtered data file. 2020-06-17 17:59:25,704:INFO:root:Wrote PCA transformed file. 2020-06-17 17:59:25,770:INFO:root:Wrote PCA components file. 2020-06-17 17:59:25,770:INFO:root:PCA transformed data. 2020-06-17 17:59:25,770:INFO:root:Will call vbgmm with parameters: Concocut_output/, 400, 1000

Installtion conda create -n concoct_env python=2.7 concoct conda activate concoct_env python /Users/tsukamotoyuuya/opt/miniconda3/envs/concoct_env/scripts/cut_up_fasta.py MZ_maxbin2_merge.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa python /Users/tsukamotoyuuya/opt/miniconda3/envs/concoct_env/scripts/concoct_coverage_table.py contigs_10K.bed hoge.sort.bam > coverage_table.tsv

concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b Concocut_output/ Up and running. Check /Volumes/HDPH-UT/Metagenome_Mizusawa_black/Raw_fastq/Concocut_output/log.txt for progress /Users/tsukamotoyuuya/opt/miniconda3/envs/concoct_env/lib/python2.7/site-packages/concoct/input.py:82: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. cov = p.read_table(cov_file, header=0, index_col=0)

conda env export

dependencies:

• alabaster=0.7.12=py27_0
• asn1crypto=1.3.0=py27_0
• babel=2.8.0=py_0
• biopython=1.68=py27_0
• blas=1.0=mkl
• brotlipy=0.7.0=py27h0b31af3_1000
• ca-certificates=2020.1.1=0
• certifi=2019.11.28=py27_0
• cffi=1.11.5=py27_0
• chardet=3.0.4=py27_1003
• concoct=0.4.2=py27hd1ccf6d_0
• cryptography=2.8=py27ha12b0ac_0
• cython=0.29.14=py27h0a44026_0
• docutils=0.15.2=py27_0
• enum34=1.1.6=py27_1
• freetype=2.10.2=ha233b18_0
• gsl=2.2.1=h002c638_3
• idna=2.8=py27_0
• imagesize=1.2.0=py_0
• intel-openmp=2019.4=233
• ipaddress=1.0.23=py_0
• jinja2=2.11.2=py_0
• jpeg=9b=he5867d9_2
• libcxx=10.0.0=1
• libedit=3.1.20191231=haf1e3a3_0
• libffi=3.3=h0a44026_1
• libgfortran=3.0.1=h93005f0_2
• libpng=1.6.37=ha441bb4_0
• libtiff=4.1.0=hcb84e12_1
• lz4-c=1.9.2=h0a44026_0
• markupsafe=1.1.1=py27h1de35cc_0
• mkl=2019.4=233
• mkl-service=2.3.0=py27hfbe908c_0
• mkl_fft=1.0.15=py27h5e564d8_0
• mkl_random=1.1.0=py27ha771720_0
• mmtf-python=1.0.2=py27_0
• msgpack-python=0.6.1=py27h04f5b5a_1
• ncurses=6.2=h0a44026_1
• nose=1.3.7=py27_2
• numpy=1.16.6=py27h81c90fd_0
• numpy-base=1.16.6=py27h6575580_0
• olefile=0.46=py27_0
• openblas=0.2.20=8
• openssl=1.1.1g=h1de35cc_0
• packaging=20.4=py_0
• pandas=0.24.2=py27h0a44026_0
• pillow=6.2.1=py27hb68e598_0
• pip=19.3.1=py27_0
• pycparser=2.20=py_0
• pygments=2.5.2=py_0
• pyopenssl=19.1.0=py27_0
• pyparsing=2.4.7=py_0
• pysocks=1.7.1=py27_0
• python=2.7.18=h47d645e_1
• python-dateutil=2.8.1=py_0
• pytz=2020.1=py_0
• readline=8.0=h1de35cc_0
• reportlab=3.5.26=py27hdea1bd8_0
• requests=2.22.0=py27_1
• scikit-learn=0.20.3=py27h27c97d8_0
• scipy=1.2.1=py27h1410ff5_0
• setuptools=44.0.0=py27_0
• six=1.15.0=py_0
• snowballstemmer=2.0.0=py_0
• sphinx=1.8.5=py27_0
• sphinx_rtd_theme=0.4.3=py_0
• sphinxcontrib=1.0=py27_1
• sphinxcontrib-websupport=1.2.1=py_0
• sqlite=3.32.2=hffcf06c_0
• tk=8.6.10=hb0a8c7a_0
• typing=3.5.2.2=py27_0
• urllib3=1.25.9=py_0
• wheel=0.33.6=py27_0
• xz=5.2.5=h1de35cc_0
• zlib=1.2.11=h1de35cc_3
• zstd=1.4.4=h1990bb4_3 prefix: /Users/tsukamotoyuuya/opt/miniconda3/envs/concoct_env**

[drish91]

I'm having the same issue with concoct where it's been running for ~2 days now and the log says it's stuck at the "vbgmm" step. I'm running version concoct 1.1.0 on 4 threads.

2021-10-19 23:34:18,230:INFO:root:Results created at /local/scratch/concoct_output/sample1/concoct 2021-10-19 23:49:22,004:INFO:root:Successfully loaded composition data. 2021-10-19 23:49:31,373:INFO:root:Successfully loaded coverage data. 2021-10-19 23:50:16,004:INFO:root:Performed PCA, resulted in 86 dimensions 2021-10-20 00:09:20,159:INFO:root:Wrote original filtered data file. 2021-10-20 00:21:11,883:INFO:root:Wrote PCA transformed file. 2021-10-20 00:21:11,903:INFO:root:Wrote PCA components file. 2021-10-20 00:21:11,903:INFO:root:PCA transformed data. 2021-10-20 00:21:11,903:INFO:root:Will call vbgmm with parameters: /local/scratch/concoct_output/sample1/concoct/, 400, 200, 8, 500

Any help appreciated!

[francesco-ricci]

Any solution to this? I am having the same problem.

Cheers Francesco