Comments (4)
Arts-of-coding
commented on August 17, 2024
Hi @janursa,
Can you provide the output of this log file?
/beegfs/desy/user/nourisaj/op_multiomics_grn/output/infer/ananse6/binding/log_Myeloid-cells.txt
I noticed that you have specified the "tmpdir" at its default location. It might help if the tmpdir is specified on a non-default location where there is certainly enough space. You can run this following command directly before the anansnake step: export TMPDIR=/...../tmp/
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janursa
commented on August 17, 2024
Regarding the default /tmp/, i checked it and it has enough space.
The log_Myeloid-cells.txt has the following content.
Matplotlib is building the font cache; this may take a moment.
2024-03-25 19:58:24 | INFO | Loading specified motif file: /beegfs/desy/user/nourisaj/op_multiomics_grn/output/infer/ananse6/gimme/hg38.gimme.vertebrate.v5.0.pfm
2024-03-25 19:58:39 | INFO | Using motifs for 828 factors
2024-03-25 19:58:45 | INFO | Loading pre-scanned motif scores
2024-03-25 19:59:40 | INFO | Using 135358 regions
2024-03-25 19:59:40 | INFO | Loading ATAC data
2024-03-25 19:59:40 | INFO | Using 1 columns
2024-03-25 19:59:41 | WARNING | Expected region width is 200, got 841.
2024-03-25 19:59:41 | DEBUG | Quantile normalization for ATAC
2024-03-25 19:59:45 | INFO | Columns being used for model type: ['ATAC', 'motif']
2024-03-25 19:59:45 | INFO | Loading models
2024-03-25 19:59:47 | INFO | Using 238 models
2024-03-25 19:59:49 | INFO | Predicting TF activity
2024-03-25 19:59:49 | INFO | Motif activity prediction on ATAC data, run 1/3
2024-03-25 19:59:58,494 - INFO - motif scanning (scores)
2024-03-25 19:59:58,494 - INFO - reading table
2024-03-25 20:00:12,414 - INFO - creating score table (z-score, GC%)
2024-03-25 20:56:31,074 - INFO - done
2024-03-25 20:56:31,075 - INFO - creating dataframe
2024-03-25 20:56:54,848 - INFO - Fitting BayesianRidge
0%| | 0/1 [00:00<?, ?it/s]
100%|██████████| 1/1 [00:47<00:00, 47.39s/it]
100%|██████████| 1/1 [00:47<00:00, 47.39s/it]
2024-03-25 20:57:51,310 - INFO - Done
2024-03-25 20:57:51 | INFO | Motif activity prediction on ATAC data, run 2/3
2024-03-25 20:58:00,260 - INFO - motif scanning (scores)
2024-03-25 20:58:00,261 - INFO - reading table
2024-03-25 20:58:05,182 - INFO - using 14000 sequences
2024-03-25 20:58:05 | INFO | Motif activity prediction on ATAC data, run 3/3
2024-03-25 20:58:13,983 - INFO - motif scanning (scores)
2024-03-25 20:58:13,983 - INFO - reading table```
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Arts-of-coding
commented on August 17, 2024
Hi @janursa,
That is good to check. I noticed that you get a warning of the expected region width (841bp instead of 200 bp peaks), which implies that either these regions are no peaks or they are very broad peaks. Since the "reading table" is after the "Fitting BayesianRidge", it might be related to a previous issue: ANANSE issue 90. Could this still be a problem @siebrenf?
For now I would suggest to try anansnake out with the example data or the constructed data (with 200bp peaks) from the anansescanpy package.
If this works, that means that your peak length needs to be trimmed. I would suggest to use snapatac2 for generating a cellxpeak matrix. Alternatively, you can create this matrix with Seurat and Signac in R, see vignette.
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janursa
commented on August 17, 2024
it turned out that there was something problematic with the installation. i reinstalled the package and everything went through.
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