lp2
commented
2 years ago 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,
=%.1f 2)0.5), w1.mean(), SP.median((w2-w12)*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]=%.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, =%.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 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
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/felicityallen/JACKS/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADIQI6XOACLLJVE747LUE3ULGUQ7ANCNFSM5HWQIMGA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
sum732
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