Bin_refinement erro about running CheckM

wanqiangdehuoguo commented 2 years ago

I want to use metawrap to bin, and i have already finished binning with concoct maxbin2 and metabat2. This is my bin results folder: $ tree INITIAL_BINNING/*_bins INITIAL_BINNING/concoct_bins ├── bin.0.fa ├── bin.100.fa ├── bin.101.fa ├── bin.102.fa ...... └── unbinned.fa INITIAL_BINNING/maxbin2_bins ├── bin.0.fa ├── bin.100.fa ├── bin.101.fa ├── bin.102.fa ├── bin.103.fa ├── bin.104.fa ...... INITIAL_BINNING/metabat2_bins ├── bin.10.fa ├── bin.11.fa ├── bin.12.fa ├── bin.13.fa ├── bin.14.fa ├── bin.15.fa ├── bin.16.fa ├── bin.17.fa ├── bin.18.fa ├── bin.19.fa ...... └── bin.unbinned.fa

and i used : nohup metawrap bin_refinement -o BIN_REFINEMENT -t 100 -A INITIAL_BINNING/metabat2_bins/ -B INITIAL_BINNING/maxbin2_bins/ -C INITIAL_BINNING/concoct_bins/ -c 70 -x 5 &

But i faced error : '''$ cat nohup.out metawrap bin_refinement -o BIN_REFINEMENT -t 100 -A INITIAL_BINNING/metabat2_bins/ -B INITIAL_BINNING/maxbin2_bins/ -C INITIAL_BINNING/concoct_bins / -c 70 -x 5

----- There is 40 RAM and 100 threads available, and each pplacer thread uses >40GB, so I will ----- ----- use 1 threads for pplacer -----

########################################################################################################################

BEGIN PIPELINE!

########################################################################################################################

.........

########################################################################################################################

BEGIN BIN REFINEMENT

########################################################################################################################

----- There are three bin folders, so there 4 ways we can refine the bins (A+B, B+C, A+C, ----- ----- A+B+C). Will try all four in parallel! -----

.........

########################################################################################################################

RUNNING CHECKM ON ALL SETS OF BINS

########################################################################################################################

----- Running CheckM on binsA bins -----

[2022-03-28 21:13:25] INFO: CheckM v1.0.18 [2022-03-28 21:13:25] INFO: checkm lineage_wf -x fa binsA binsA.checkm -t 100 --tmpdir binsA.tmp --pplacer_threads 1

.........

----- There are 0 'good' bins found in binsA! (>70% completion and <5% contamination) -----

----- Running CheckM on binsAB bins -----

.........

----- There are 0 'good' bins found in binsAB! (>70% completion and <5% contamination) -----

----- Running CheckM on binsABC bins -----

........................................

[2022-03-28 22:45:42] INFO: { Current stage: 0:00:58.012 || Total: 0:20:47.285 }

----- There are 0 'good' bins found in binsC! (>70% completion and <5% contamination) -----

########################################################################################################################

CONSOLIDATING ALL BIN SETS BY CHOOSING THE BEST VERSION OF EACH BIN

########################################################################################################################

----- There are 3 original bin folders, plus the refined bins. -----

rm: cannot remove 'binsM': No such file or directory rm: cannot remove 'binsM.stats': No such file or directory

----- merging binsABC.stats and binsM -----

Loading list of good bins (comp>70.0%, cont<5.0%) load in the info about the contigs in each bin... make all bossible comparisons between the two bin sets, and record total % idential length load in completion and contamination scores of all the bins go through first group, pull out identical bins from second group, and choose best retrieve bins from second group that were not found in first group There were 1 bins cherry-picked from the original sets!

...........

########################################################################################################################

FINALIZING THE REFINED BINS

########################################################################################################################

----- Re-running CheckM on binsO bins -----

[2022-03-28 22:45:43] INFO: CheckM v1.0.18 [2022-03-28 22:45:43] INFO: checkm lineage_wf -x fa binsO binsO.checkm -t 100 --tmpdir binsO.tmp --pplacer_threads 1 [2022-03-28 22:45:43] INFO: [CheckM - tree] Placing bins in reference genome tree. [2022-03-28 22:45:43] ERROR: No bins found. Check the extension (-x) used to identify bins.

Controlled exit resulting from an unrecoverable error or warning.

Something went wrong with running CheckM. Exiting...

'''

My question is, is it because I set "-c 70-x 5" too high and my data is not good that bin_refinement error occurs, or is my system having problems with conda env?How can I solve it?

By the way, I was able to run bin_refinement in an existing computer environment using the sample data in the tutorial.

Metawrap is very good to use, I hope to focus on this issue.

galodavid commented 2 years ago

Hi I am having the same issue on the bin refinement module, I know i have bins that comply with the contamination and completion requirements but it says that there are 0 good bins found, even when manually selected the bins using checkM manually after binning module, the pipeline does not show any errors and it keeps running to the other bins and samples but the folder and file of interest is empty in the output folder. please help

IMG_20220805_120624 IMG_20220805_120630

wanqiangdehuoguo commented 2 years ago

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Hi, In my opinion, I think MetaWrap made other judgments after doing checkM. My advice is to try lowering the filtering threshold, or to use a tool that is not ChecKM-based, such as DAS_tools... If you solve this issue, please tell me. Thanks a lot.

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          Re: [bxlab/metaWRAP] Bin_refinement erro about running CheckM (Issue #434)

Hi I am having the same issue on the bin refinement module, I know i have bins that comply with the contamination and completion requirements but it says that there are 0 good bins found, even when manually selected the bins using checkM manually after binning module, the pipeline does not show any errors and it keeps running to the other bins and samples but the folder and file of interest is empty in the output folder. please help

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galodavid commented 2 years ago

I tried with 30 compeltion and 30 contamination still displays the 0 good bins found.

bxlab / metaWRAP