ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module

Question

[shevch2009]

Hi! This is really strange I used

/mnt/nvme/tutukina/miniconda3/bin/metawrap binning -o /mnt/nvme/tutukina/polyfilter_results/INITIAL_BINNING_FP1 -t 10 -a /mnt/nvme/tutukina/polyfilter_results/assembly_carpedeam/FP1_polyfiltered_assembly_carpedeam.fasta --metaba2 /mnt/nvme/tutukina/polyfilter_results/CLEAN_READS_metawrap/FP1/*fastq

/mnt/nvme/tutukina/miniconda3/bin/metawrap binning -o /mnt/nvme/tutukina/polyfilter_results/INITIAL_BINNING_FP1 -t 10 -a /mnt/nvme/tutukina/polyfilter_results/assembly_carpedeam/FP1_polyfiltered_assembly_carpedeam.fasta --maxbin2 /mnt/nvme/tutukina/polyfilter_results/CLEAN_READS_metawrap/FP1/*fastq

and I got bins, but when I did the same for concoct it's not working How so?

Can anyone suggest the solution? What strange is that I did the same steps with another sample, and it worked.

I used:

/mnt/nvme/tutukina/miniconda3/bin/metawrap binning -o /mnt/nvme/tutukina/polyfilter_results/INITIAL_BINNING_FP1 -t 10 -a /mnt/nvme/tutukina/polyfilter_results/assembly_carpedeam/FP1_polyfiltered_assembly_carpedeam.fasta --concoct /mnt/nvme/tutukina/polyfilter_results/CLEAN_READS_metawrap/FP1/*fastq

and I keep getting this:

Up and running. Check /mnt/nvme/tutukina/polyfilter_results/INITIAL_BINNING_FP1/work_files/concoct_out/log.txt for progress
/mnt/nvme/tutukina/miniconda3/envs/metawrap-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)
/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/numpy/lib/arraysetops.py:569: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
mask |= (ar1 == a)
Traceback (most recent call last):
File "/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/bin/concoct", line 88, in
results = main(args)
File "/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/bin/concoct", line 40, in main
args.seed
File "/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/concoct/transform.py", line 5, in perform_pca
pca_object = PCA(n_components=nc, random_state=seed).fit(d)
File "/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/sklearn/decomposition/pca.py", line 340, in fit
self._fit(X)
File "/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/sklearn/decomposition/pca.py", line 381, in _fit
copy=self.copy)
File "/mnt/nvme/tutukina/miniconda3/envs/metawrap-env/lib/python2.7/site-packages/sklearn/utils/validation.py", line 582, in check_array
context))
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required.

***** Something went wrong with binning with CONCOCT. Exiting...

I wrote the same on githud metawrap page, but it looks like noone is answering there for a while.

Thank you. Best, Alla

[GenoMax]

Are you following the steps described in the tutorial --> https://github.com/bxlab/metaWRAP/blob/master/Usage_tutorial.md

A casual glance through your command line above does not appear to be the right way of running this analysis.

[shevch2009]

Yes, in tutorial - metawrap binning -o INITIAL_BINNING -t 96 -a ASSEMBLY/final_assembly.fasta --metabat2 --maxbin2 --concoct CLEAN_READS/ERR*fastq

The initial binning process with CONCOCT, MaxBin, and metaBAT will be the more time intensive steps (especially CONCOCT and MaxBin), so I would advise you to run the Binning module with each of the algorithms seperately.

So, I used this advice - to run separatly each binner - (metawrap-env) m_tutukina@srv21gr:~$ /mnt/nvme/tutukina/miniconda3/bin/metawrap binning -o /mnt/nvme/tutukina/polyfilter_results/INITIAL_BINNING_FP1 -t 10 -a /mnt/nvme/tutukina/polyfilter_results/assembly_carpedeam/FP1_polyfiltered_assembly_carpedeam.fasta --concoct /mnt/nvme/tutukina/polyfilter_results/CLEAN_READS_metawrap/FP1/*fastq