RuntimeWarning: Mean of empty slice #17
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Hmm, there seems to be a problem earlier, "collating 0 samples" feels like
an item of concern. I'm not sure if it is a potential mismatch in column
headings for the sgRNA in Count_Matrix.tab vs sgrna [all lower case] in
sgRNA_Mapping_File , or ability to identify the sample from sample file.
The way in which the replicate and sample are specified has been improved
over the years, so I am not completely sure what the right encoding is, but
I would think it to potentially be the main culprit. Let me know if this
does not help rapidly resolve,
Leo
…On Tue, Nov 9, 2021 at 11:24 PM sum732 ***@***.***> wrote:
Hello,
I am trying to use JACKS and running into following issues:
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File.tab --sgrna_hdr=sgrna --gene
_hdr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS
[2021-11-09 18:05:01,363] jacks: INFO Loading sample specification
[2021-11-09 18:05:01,363] jacks: INFO Loading gene mappings
[2021-11-09 18:05:01,365] jacks: INFO Loading data and pre-processing
[2021-11-09 18:05:01,424] jacks: INFO Applying median normalisation
[2021-11-09 18:05:01,471] jacks: INFO Collating 0 samples
[2021-11-09 18:05:01,487] jacks: INFO Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, **kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-09 18:05:01,801] jacks: INFO Writing JACKS results
/gpfs/fs1/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
Here are snippets of how various files look:
head -n +4 Count_Matrix.tab
sgRNA P23H1 P23H2 Control1 Control2 Control3
Amfr_sgRNA1 150 44 602 530 302
Amfr_sgRNA2 141 24 380 350 162
Amfr_sgRNA3 203 21 443 435 303
head Exp_Summary_JACKS.tab
Replicate Sample
P23H1 P23H
P23H2 P23H
Control1 CTRL
Control2 CTRL
Control3 CTRL
head -n +3 sgRNA_Mapping_File.tab
sgrna Gene
Sec24d_sgRNA2 Sec24d
Gm30534_sgRNA3 Gm30534
Not exactly why any array slice will produce a mean of <0( assuming that
is the error). The counts is tab separated and so are the other files as
well.
Any help will be much appreciated.
Thanks,
D
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Hi Leo, Got this error Changed to Match Error Here is Expsummary These all are tab separated, I reconfirmed this. |
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Just to triple check - did you use the latest version, and have you tried
explicitly setting
--rep_hdr=Replicate --sample_hdr=Sample
? The --ctrl-sample-hdr is for the third header, I worry if the defaults
for first two match what you use.
https://github.com/felicityallen/JACKS/tree/master/jacks has the example
…On Thu, Nov 11, 2021 at 10:50 PM sum732 ***@***.***> wrote:
Hi Leo,
Thank you for responding and for the suggestion.
I had tried setting things correctly
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgrna Gene P23H_rep1 P23H_rep2 Control_rep1 Control_rep2 Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <==
sgrna Gene
Got this error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgrna --gene_h
dr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS
[2021-11-11 17:39:54,074] jacks: INFO Loading sample specification
[2021-11-11 17:39:54,075] jacks: INFO Loading gene mappings
[2021-11-11 17:39:54,078] jacks: INFO Loading data and pre-processing
[2021-11-11 17:39:54,136] jacks: INFO Applying median normalisation
[2021-11-11 17:39:54,184] jacks: INFO Collating 0 samples
[2021-11-11 17:39:54,200] jacks: INFO Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, **kwargs)
/homes/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/gpfs/fs1/home/mehrotras/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:39:54,511] jacks: INFO Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
(jacksenv) ***@***.***:$/JACKS>head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
Changed to Match
head -n +1 Count_Matrix-Fixed.tab sgRNA_Mapping_File-Fixed.tab
==> Count_Matrix-Fixed.tab <==
sgRNA Gene P23H_rep1 P23H_rep2 Control_rep1 Control_rep2 Control_rep3
==> sgRNA_Mapping_File-Fixed.tab <==
sgRNA Gene
Error
python ~/Research/Programs/Jacks/JACKS/jacks/run_JACKS.py Count_Matrix-Fixed.tab Exp_Summary_JACKS.tab sgRNA_Mapping_File-Fixed.tab --sgrna_hdr=sgRNA --gene_hdr=Gene --ctrl_sample_hdr=Sample --outprefix JACKS
[2021-11-11 17:42:37,162] jacks: INFO Loading sample specification
[2021-11-11 17:42:37,162] jacks: INFO Loading gene mappings
[2021-11-11 17:42:37,164] jacks: INFO Loading data and pre-processing
[2021-11-11 17:42:37,223] jacks: INFO Applying median normalisation
[2021-11-11 17:42:37,272] jacks: INFO Collating 0 samples
[2021-11-11 17:42:37,288] jacks: INFO Running JACKS inference
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/scipy/_lib/deprecation.py:20: RuntimeWarning: Mean of empty slice
return fun(*args, **kwargs)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:88: RuntimeWarning: Mean of empty slice.
LOG.debug("After init, mean absolute error=%.3f, <x>=%.1f <w>=%.1f lower bound=%.1f"%(SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), w1.mean(), bound))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:115: RuntimeWarning: Mean of empty slice.
LOG.debug("After W update, <w>=%.1f, mean absolute error=%.3f"%(w1.mean(), SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean()))
/home/Research/Programs/Jacks/JACKS/jacks/jacks/infer.py:96: RuntimeWarning: Mean of empty slice.
LOG.debug("Iter %d/%d. lb: %.1f err: %.3f x:%.2f+-%.2f w:%.2f+-%.2f xw:%.2f"%(i+1, n_iter, bound, SP.nanmean(abs(y.T-SP.outer(w1,x1))).mean(), x1.mean(), SP.median((x2-x1**2)**0.5), w1.mean(), SP.median((w2-w1**2)**0.5), x1.mean()*w1.mean()))
/home/.conda/envs/jacksenv/lib/python3.10/site-packages/numpy/core/fromnumeric.py:3440: RuntimeWarning: Mean of empty slice.
return _methods._mean(a, axis=axis, dtype=dtype,
[2021-11-11 17:42:37,602] jacks: INFO Writing JACKS results
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:28: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
/home/Research/Programs/Jacks/JACKS/jacks/jacks/jacks_io.py:137: RuntimeWarning: Mean of empty slice
ordered_genes = [(np.nanmean(jacks_results[gene][4]),gene) for gene in jacks_results]
Here is Expsummary
cat Exp_Summary_JACKS.tab
Replicate Sample
P23H_rep1 P23H
P23H_rep2 P23H
Control_rep1 CTRL
Control_rep2 CTRL
Control_rep3 CTRL
These all are tab separated, I reconfirmed this.
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Hi Leo, I am getting So it seems that I need the third column. However, I am not sure how set this correctly. I have 3 WT/Controls and 2 muts/treatments. Making this change shows following error |
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Hello,
I am trying to use JACKS and running into following issues:
Here are snippets of how various files look:
head -n +4 Count_Matrix.tab
head Exp_Summary_JACKS.tab
head -n +3 sgRNA_Mapping_File.tab
Not exactly sure why any array slice will produce a mean of <0( assuming that is the error). The counts is tab separated and so are the other files as well. I do see a
Collating 0 samplescould this be the issue?Any help will be much appreciated.
Thanks,
D
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