Hello,
I have been getting an error running BINDetect- this error still occurs when suing entirely test data so is not an issue with input data.
_TOBIAS BINDetect --motifs test_data/motifs.jaspar --signals test_data/Bcell_footprints.bw --genome test_data/genome.fa.gz --peaks test_data/merged_peaks_annotated.bed --peak_header test_data/merged_peaks_annotated_header.txt --outdir BINDetect_single_output --cond_names Bcell --cores 8
TOBIAS 0.17.3 BINDetect (run started 2026-03-10 17:15:27.889897)
Working directory: /gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts
Command line call: TOBIAS BINDetect --motifs test_data/motifs.jaspar --signals test_data/Bcell_footprints.bw --genome test_data/genome.fa.gz --peaks test_data/merged_peaks_annotated.bed --peak_header test_data/merged_peaks_annotated_header.txt --outdir BINDetect_single_output --cond_names Bcell --cores 8
----- Input parameters -----
signals: ['test_data/Bcell_footprints.bw']
peaks: test_data/merged_peaks_annotated.bed
motifs: ['test_data/motifs.jaspar']
genome: test_data/genome.fa.gz
cond_names: ['Bcell']
peak_header: test_data/merged_peaks_annotated_header.txt
naming: name_id
motif_pvalue: 0.0001
bound_pvalue: 0.001
cluster_threshold: 0.5
pseudo: None
time_series: False
skip_excel: False
output_peaks: None
norm_off: False
prefix: bindetect
outdir: /gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output
cores: 8
split: 100
debug: False
verbosity: 3
----- Output files -----
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//beds/_Bcell_bound.bed
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//beds/_Bcell_unbound.bed
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//beds/_all.bed
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//plots/_log2fcs.pdf
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//_overview.txt
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//_overview.xlsx
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_distances.txt
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_results.txt
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_results.xlsx
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_figures.pdf
2026-03-10 17:15:27 (3052265) [INFO] ----- Processing input data -----
2026-03-10 17:15:27 (3052265) [INFO] Checking reading/writing of files
2026-03-10 17:15:27 (3052265) [INFO] Reading peaks
2026-03-10 17:15:28 (3052265) [INFO] - Found 6007 regions in input peaks
2026-03-10 17:15:28 (3052265) [INFO] - Merged to 6007 regions
2026-03-10 17:15:28 (3052265) [INFO] Checking for match between --peaks and --fasta/--signals boundaries
2026-03-10 17:15:28 (3052265) [INFO] - Comparing peaks to test_data/genome.fa.gz
2026-03-10 17:15:28 (3052265) [INFO] - Comparing peaks to test_data/Bcell_footprints.bw
2026-03-10 17:15:28 (3052265) [INFO] Estimating GC content from peak sequences
2026-03-10 17:15:28 (3052265) [INFO] - GC content estimated at 47.61%
2026-03-10 17:15:28 (3052265) [INFO] Reading motifs from file
2026-03-10 17:15:28 (3052265) [INFO] - Read 83 motifs
2026-03-10 17:15:28 (3052265) [INFO] Creating folder structure for each TF
2026-03-10 17:15:28 (3052265) [INFO] Plotting sequence logos for each motif
2026-03-10 17:15:28 (3052265) [INFO] Progress 0%
2026-03-10 17:15:28 (3052265) [INFO] Progress 100.0%
2026-03-10 17:15:28 (3052265) [INFO] Progress done!
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 2144, in _setitem_single_column
self.obj._mgr.column_setitem(
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 1518, in column_setitem
col_mgr.setitem_inplace(idx, value)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 2220, in setitem_inplace
value = np_can_hold_element(arr.dtype, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/dtypes/cast.py", line 1705, in np_can_hold_element
raise LossySetitemError
pandas.errors.LossySetitemError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/utils/motifs.py", line 1030, in logo_to_file
logo = self.create_logo(ylim=ylim) #returns a logo object
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/utils/motifs.py", line 1067, in create_logo
info_df = logomaker.transform_matrix(df, from_type="counts", to_type="information")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/logomaker/src/error_handling.py", line 102, in wrapped_func
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/logomaker/src/matrix.py", line 228, in transform_matrix
prob_df = _counts_mat_to_probability_mat(df, pseudocount)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/logomaker/src/matrix.py", line 270, in _counts_mat_to_probability_mat
prob_df.loc[:, :] = vals / vals.sum(axis=1)[:, np.newaxis]
~~~~~~~~~~~^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 938, in setitem
iloc._setitem_with_indexer(indexer, value, self.name)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1953, in _setitem_with_indexer
self._setitem_with_indexer_split_path(indexer, value, name)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1993, in _setitem_with_indexer_split_path
self._setitem_with_indexer_2d_value(indexer, value)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 2066, in _setitem_with_indexer_2d_value
self._setitem_single_column(loc, value_col, pi)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 2163, in _setitem_single_column
raise TypeError(
TypeError: Invalid value '[3.52543464e-01 2.93750000e-01 2.33463035e-03 4.43211247e-01
9.93583868e-01 2.26860254e-03 8.66811280e-01 8.09388911e-02
2.10014948e-01 2.61682243e-01 1.19256401e-02 2.75709953e-04
8.22015726e-03 4.53889943e-01 3.66132723e-03 1.36986301e-02
1.54924515e-01]' for dtype 'int64'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/bin/TOBIAS", line 11, in
sys.exit(main())
^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/TOBIAS.py", line 163, in main
args.func(args)
^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/tools/bindetect.py", line 299, in run_bindetect
results = [task.get() for task in task_list]
^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/multiprocessing/pool.py", line 774, in get
raise self.value
TypeError: Invalid value '[3.52543464e-01 2.93750000e-01 2.33463035e-03 4.43211247e-01
9.93583868e-01 2.26860254e-03 8.66811280e-01 8.09388911e-02
2.10014948e-01 2.61682243e-01 1.19256401e-02 2.75709953e-04
8.22015726e-03 4.53889943e-01 3.66132723e-03 1.36986301e-02
1.54924515e-01]' for dtype 'int64'
The error still persists after creating a fresh conda environment and reinstalling TOBIAS using condo install -c bioconda tobias.
Any help or insights very appreciated, thank you.
Hello,
I have been getting an error running BINDetect- this error still occurs when suing entirely test data so is not an issue with input data.
_TOBIAS BINDetect --motifs test_data/motifs.jaspar --signals test_data/Bcell_footprints.bw --genome test_data/genome.fa.gz --peaks test_data/merged_peaks_annotated.bed --peak_header test_data/merged_peaks_annotated_header.txt --outdir BINDetect_single_output --cond_names Bcell --cores 8
TOBIAS 0.17.3 BINDetect (run started 2026-03-10 17:15:27.889897)
Working directory: /gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts
Command line call: TOBIAS BINDetect --motifs test_data/motifs.jaspar --signals test_data/Bcell_footprints.bw --genome test_data/genome.fa.gz --peaks test_data/merged_peaks_annotated.bed --peak_header test_data/merged_peaks_annotated_header.txt --outdir BINDetect_single_output --cond_names Bcell --cores 8
----- Input parameters -----
signals: ['test_data/Bcell_footprints.bw']
peaks: test_data/merged_peaks_annotated.bed
motifs: ['test_data/motifs.jaspar']
genome: test_data/genome.fa.gz
cond_names: ['Bcell']
peak_header: test_data/merged_peaks_annotated_header.txt
naming: name_id
motif_pvalue: 0.0001
bound_pvalue: 0.001
cluster_threshold: 0.5
pseudo: None
time_series: False
skip_excel: False
output_peaks: None
norm_off: False
prefix: bindetect
outdir: /gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output
cores: 8
split: 100
debug: False
verbosity: 3
----- Output files -----
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//beds/_Bcell_bound.bed
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//beds/_Bcell_unbound.bed
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//beds/_all.bed
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//plots/_log2fcs.pdf
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//_overview.txt
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output//_overview.xlsx
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_distances.txt
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_results.txt
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_results.xlsx
/gpfs/igmmfs01/eddie/semple-lab/stimmins/TOBIAS_briscoe/briscoe-nf-tobias/scripts/BINDetect_single_output/bindetect_figures.pdf
2026-03-10 17:15:27 (3052265) [INFO] ----- Processing input data -----
2026-03-10 17:15:27 (3052265) [INFO] Checking reading/writing of files
2026-03-10 17:15:27 (3052265) [INFO] Reading peaks
2026-03-10 17:15:28 (3052265) [INFO] - Found 6007 regions in input peaks
2026-03-10 17:15:28 (3052265) [INFO] - Merged to 6007 regions
2026-03-10 17:15:28 (3052265) [INFO] Checking for match between --peaks and --fasta/--signals boundaries
2026-03-10 17:15:28 (3052265) [INFO] - Comparing peaks to test_data/genome.fa.gz
2026-03-10 17:15:28 (3052265) [INFO] - Comparing peaks to test_data/Bcell_footprints.bw
2026-03-10 17:15:28 (3052265) [INFO] Estimating GC content from peak sequences
2026-03-10 17:15:28 (3052265) [INFO] - GC content estimated at 47.61%
2026-03-10 17:15:28 (3052265) [INFO] Reading motifs from file
2026-03-10 17:15:28 (3052265) [INFO] - Read 83 motifs
2026-03-10 17:15:28 (3052265) [INFO] Creating folder structure for each TF
2026-03-10 17:15:28 (3052265) [INFO] Plotting sequence logos for each motif
2026-03-10 17:15:28 (3052265) [INFO] Progress 0%
2026-03-10 17:15:28 (3052265) [INFO] Progress 100.0%
2026-03-10 17:15:28 (3052265) [INFO] Progress done!
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 2144, in _setitem_single_column
self.obj._mgr.column_setitem(
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 1518, in column_setitem
col_mgr.setitem_inplace(idx, value)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 2220, in setitem_inplace
value = np_can_hold_element(arr.dtype, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/dtypes/cast.py", line 1705, in np_can_hold_element
raise LossySetitemError
pandas.errors.LossySetitemError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/utils/motifs.py", line 1030, in logo_to_file
logo = self.create_logo(ylim=ylim) #returns a logo object
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/utils/motifs.py", line 1067, in create_logo
info_df = logomaker.transform_matrix(df, from_type="counts", to_type="information")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/logomaker/src/error_handling.py", line 102, in wrapped_func
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/logomaker/src/matrix.py", line 228, in transform_matrix
prob_df = _counts_mat_to_probability_mat(df, pseudocount)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/logomaker/src/matrix.py", line 270, in _counts_mat_to_probability_mat
prob_df.loc[:, :] = vals / vals.sum(axis=1)[:, np.newaxis]
~~~~~~~~~~~^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 938, in setitem
iloc._setitem_with_indexer(indexer, value, self.name)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1953, in _setitem_with_indexer
self._setitem_with_indexer_split_path(indexer, value, name)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 1993, in _setitem_with_indexer_split_path
self._setitem_with_indexer_2d_value(indexer, value)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 2066, in _setitem_with_indexer_2d_value
self._setitem_single_column(loc, value_col, pi)
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/pandas/core/indexing.py", line 2163, in _setitem_single_column
raise TypeError(
TypeError: Invalid value '[3.52543464e-01 2.93750000e-01 2.33463035e-03 4.43211247e-01
9.93583868e-01 2.26860254e-03 8.66811280e-01 8.09388911e-02
2.10014948e-01 2.61682243e-01 1.19256401e-02 2.75709953e-04
8.22015726e-03 4.53889943e-01 3.66132723e-03 1.36986301e-02
1.54924515e-01]' for dtype 'int64'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/bin/TOBIAS", line 11, in
sys.exit(main())
^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/TOBIAS.py", line 163, in main
args.func(args)
^^^^^^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/site-packages/tobias/tools/bindetect.py", line 299, in run_bindetect
results = [task.get() for task in task_list]
^^^^^^^^^^
File "/exports/eddie/scratch/s2559269/anaconda/envs/tobias_nf2/lib/python3.12/multiprocessing/pool.py", line 774, in get
raise self.value
TypeError: Invalid value '[3.52543464e-01 2.93750000e-01 2.33463035e-03 4.43211247e-01
9.93583868e-01 2.26860254e-03 8.66811280e-01 8.09388911e-02
2.10014948e-01 2.61682243e-01 1.19256401e-02 2.75709953e-04
8.22015726e-03 4.53889943e-01 3.66132723e-03 1.36986301e-02
1.54924515e-01]' for dtype 'int64'
The error still persists after creating a fresh conda environment and reinstalling TOBIAS using condo install -c bioconda tobias.
Any help or insights very appreciated, thank you.