How to resolve There are 0 'good' bins found in binsA! ?

[mathavanpu]

Hello,
I am running the metro wrap pipeline, In the bin refinement step I got the error mentioned below, kindly help me to solve it

----- There are 0 'good' bins found in binsA! (>50% completion and <10% contamination) -----

metawrap bin_refinement -o BIN_REFINEMENT -t 96 -A INITIAL_BINNING/metabat2_bins/ -B INITIAL_BINNING/maxbin2_bins/ -C INITIAL_BINNING/concoct_bins/ -c 50 -x 10

---

----- There is 40 RAM and 96 threads available, and each pplacer thread uses >40GB, so I will -----
----- use 1 threads for pplacer -----

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

BEGIN PIPELINE!

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

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----- setting up output folder and copything over bins... -----

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----- there are 5 bins in binsA -----

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----- there are 10 bins in binsB -----

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----- there are 18 bins in binsC -----

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----- There are 3 bin sets! -----

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----- Fix contig naming by removing special characters... -----

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

BEGIN BIN REFINEMENT

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

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----- 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! -----

Specified 2 input bin sets: -1 binsC -2 binsB
Specified 3 input bin sets: -1 binsA -2 binsB -3 binsC
Specified 2 input bin sets: -1 binsA -2 binsB
Specified 2 input bin sets: -1 binsA -2 binsC
Add folder/bin name to contig name for binsA bins
Add folder/bin name to contig name for binsC bins
Add folder/bin name to contig name for binsA bins
Add folder/bin name to contig name for binsA bins
Add folder/bin name to contig name for binsB bins
Add folder/bin name to contig name for binsB bins
Add folder/bin name to contig name for binsC bins
Add folder/bin name to contig name for binsB bins
Add folder/bin name to contig name for binsC bins
Combine all bins together
Combine all bins together
Combine all bins together
The number of refined bins: 8
Combine all bins together
The number of refined bins: 8
The number of refined bins: 5
Exporting refined bins...
Exporting refined bins...
Exporting refined bins...
The number of refined bins: 8
Exporting refined bins...
Extracting refined bin: Refined_5.fasta
Deleting temporary files
Extracting refined bin: Refined_8.fasta
Deleting temporary files
Extracting refined bin: Refined_8.fasta
Deleting temporary files

All done!

All done!

All done!
Extracting refined bin: Refined_8.fasta
Deleting temporary files

All done!

---

----- there are 8 refined bins in binsAB -----

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----- there are 8 refined bins in binsBC -----

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----- there are 5 refined bins in binsAC -----

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----- there are 8 refined bins in binsABC -----

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----- Bin refinement finished successfully! -----

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----- fixing bin naming to .fa convention for consistancy... -----

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

RUNNING CHECKM ON ALL SETS OF BINS

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

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

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[CheckM - tree] Placing bins in reference genome tree.

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Identifying marker genes in 5 bins with 96 threads:
Finished processing 5 of 5 (100.00%) bins.
Traceback (most recent call last):
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/multiprocessing/util.py", line 277, in _run_finalizers
finalizer()
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/multiprocessing/util.py", line 207, in call
res = self._callback(*self._args, **self._kwargs)
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/shutil.py", line 266, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/shutil.py", line 264, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'binsA.tmp/pymp-RDJNFU/.nfs00000000315c43c8001d0958'
Saving HMM info to file.

Calculating genome statistics for 5 bins with 96 threads:
Finished processing 5 of 5 (100.00%) bins.

Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 5 of 5 (100.00%) bins.
Extracting 43 HMMs with 96 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 96 threads:
Finished aligning 43 of 43 (100.00%) marker genes.

Reading marker alignment files.
Concatenating alignments.
Placing 5 bins into the genome tree with pplacer (be patient).

{ Current stage: 0:05:24.184 || Total: 0:05:24.184 }

---

[CheckM - lineage_set] Inferring lineage-specific marker sets.

---

Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 5 of 5 (100.00%) bins.

Determining marker sets for each genome bin.
Finished processing 5 of 5 (100.00%) bins (current: bin.1).

Marker set written to: binsA.checkm/lineage.ms

{ Current stage: 0:00:03.744 || Total: 0:05:27.929 }

---

[CheckM - analyze] Identifying marker genes in bins.

---

Identifying marker genes in 5 bins with 96 threads:
Finished processing 5 of 5 (100.00%) bins.
Traceback (most recent call last):
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/multiprocessing/util.py", line 277, in _run_finalizers
finalizer()
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/multiprocessing/util.py", line 207, in call
res = self._callback(*self._args, **self._kwargs)
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/shutil.py", line 266, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/shutil.py", line 264, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'binsA.tmp/pymp-I2JuJq/.nfs00000000315c4492001d095e'
Saving HMM info to file.

{ Current stage: 0:01:52.185 || Total: 0:07:20.114 }

Parsing HMM hits to marker genes:
Finished parsing hits for 5 of 5 (100.00%) bins.
Aligning marker genes with multiple hits in a single bin:
Finished processing 5 of 5 (100.00%) bins.

{ Current stage: 0:00:23.708 || Total: 0:07:43.822 }

Calculating genome statistics for 5 bins with 96 threads:
Finished processing 5 of 5 (100.00%) bins.

{ Current stage: 0:00:06.442 || Total: 0:07:50.265 }

---

[CheckM - qa] Tabulating genome statistics.

---

Calculating AAI between multi-copy marker genes.

Reading HMM info from file.
Parsing HMM hits to marker genes:
Finished parsing hits for 5 of 5 (100.00%) bins.

---

Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity

bin.unbinned k__Bacteria (UID203) 5449 104 58 19 21 28 12 15 9 73.85 91.49 16.84
bin.1 p__Actinobacteria (UID1454) 732 199 116 86 85 27 1 0 0 62.01 19.45 33.33
bin.2 k__Bacteria (UID203) 5449 104 58 84 13 7 0 0 0 11.90 2.66 42.86
bin.3 root (UID1) 5656 56 24 55 1 0 0 0 0 4.17 0.00 0.00
bin.4 root (UID1) 5656 56 24 56 0 0 0 0 0 0.00 0.00 0.00

{ Current stage: 0:00:05.052 || Total: 0:07:55.317 }

---

----- There are 0 'good' bins found in binsA! (>50% completion and <10% contamination) -----

---

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

---

[CheckM - tree] Placing bins in reference genome tree.

---

Identifying marker genes in 8 bins with 96 threads:
Finished processing 8 of 8 (100.00%) bins.
Traceback (most recent call last):
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/multiprocessing/util.py", line 277, in _run_finalizers
finalizer()
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/multiprocessing/util.py", line 207, in call
res = self._callback(*self._args, **self._kwargs)
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/shutil.py", line 266, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/apps_940/miniconda/envs/metawrap_prokka/lib/python2.7/shutil.py", line 264, in rmtree
os.remove(fullname)
OSError: [Errno 16] Device or resource busy: 'binsAB.tmp/pymp-Jh1tkP/.nfs00000000315c4649001d0967'
Saving HMM info to file.

Calculating genome statistics for 8 bins with 96 threads:
Finished processing 8 of 8 (100.00%) bins.

Extracting marker genes to align.
Parsing HMM hits to marker genes:
Finished parsing hits for 8 of 8 (100.00%) bins.
Extracting 43 HMMs with 96 threads:
Finished extracting 43 of 43 (100.00%) HMMs.
Aligning 43 marker genes with 96 threads:
Finished aligning 43 of 43 (100.00%) marker genes.

Reading marker alignment files.
Concatenating alignments.

[galodavid]

I am having the same issue can you please provide any guidance or a solution if you have it