INFO @ Sat, 29 May 2021 19:54:23: Parameters: /backup/home/changxing/anaconda3/envs/MAGeCK/bin/mageck mle --count-table BatchCorrect.txt --design-matrix designmatrix.txt --norm-method control --control-sgrna ctrl_sgrna_list.txt --output-prefix braf.mle
INFO @ Sat, 29 May 2021 19:54:23: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Sat, 29 May 2021 19:54:23: Design matrix:
INFO @ Sat, 29 May 2021 19:54:23: [[1. 1. 0. 0.]
INFO @ Sat, 29 May 2021 19:54:23: [1. 1. 0. 0.]
INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 1. 0.]
INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 1. 0.]
INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 0. 1.]
INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 0. 1.]]
INFO @ Sat, 29 May 2021 19:54:23: Beta labels:baseline,Day4,Day10,Day18
INFO @ Sat, 29 May 2021 19:54:23: Included samples:sample1_1,sample2_1,sample1_2,sample2_2,sample1_3,sample2_3
INFO @ Sat, 29 May 2021 19:54:23: Loaded samples:sample1_1;sample2_1;sample1_2;sample2_2;sample1_3;sample2_3
INFO @ Sat, 29 May 2021 19:54:23: Sample index: 0;3;1;4;2;5
INFO @ Sat, 29 May 2021 19:54:23: Loaded 7637 genes.
INFO @ Sat, 29 May 2021 19:54:23: 200 out of 200 control sgRNAs are found in count table.
INFO @ Sat, 29 May 2021 19:54:23: Loaded 200 control sgRNAs from ctrl_sgrna_list.txt
INFO @ Sat, 29 May 2021 19:54:23: control sgRNAs for normalization:200
INFO @ Sat, 29 May 2021 19:54:23: Final size factor: 0.7418480620804788 0.9801916242140984 1.22032074908657 1.3618267986174515 1.0019762721094752 0.7725871057326363
INFO @ Sat, 29 May 2021 19:54:23: size factor: 1.3479849191700333,1.020208676851104,0.8194566885374328,0.7343077702797567,0.9980276258385695,1.2943524329877476
INFO @ Sat, 29 May 2021 19:54:23: Thread 0 started.
INFO @ Sat, 29 May 2021 19:54:23: Thread 0: total 1 instances.
/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:445: RuntimeWarning: Mean of empty slice.
return N.ndarray.mean(self, axis, dtype, out, keepdims=True)._collapse(axis)
/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/core/_methods.py:162: RuntimeWarning: invalid value encountered in true_divide
ret = um.true_divide(
Process Thread 0:
Traceback (most recent call last):
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(self._args, self._kwargs)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 38, in thread_p_func
iteratenbem(tginst,iteratenbemargs)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 533, in iteratenbem
retlist=em_whileloop(sk,beta_init_mat,size_vec,wfrac_list,alpha_dispersion,alpha_val,estimateeff,updateeff,removeoutliers,debug)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 265, in em_whileloop
xwx_inv=linalg.inv(xwx_mat)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/linalg/basic.py", line 934, in inv
a1 = _asarray_validated(a, check_finite=check_finite)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/_lib/_util.py", line 262, in _asarray_validated
a = toarray(a)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/lib/function_base.py", line 485, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs
INFO @ Sat, 29 May 2021 19:54:23: Thread 0 completed.
INFO @ Sat, 29 May 2021 19:54:23: All threads completed.
INFO @ Sat, 29 May 2021 19:54:23: Modeling the mean and variance ...
INFO @ Sat, 29 May 2021 19:54:23: Run the algorithm for the second time ...
INFO @ Sat, 29 May 2021 19:54:23: Thread 0 started.
INFO @ Sat, 29 May 2021 19:54:23: Thread 0: total 7637 instances.
/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:445: RuntimeWarning: Mean of empty slice.
return N.ndarray.mean(self, axis, dtype, out, keepdims=True)._collapse(axis)
/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/core/_methods.py:162: RuntimeWarning: invalid value encountered in true_divide
ret = um.true_divide(
Process Thread 0:
Traceback (most recent call last):
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(self._args, self._kwargs)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 38, in thread_p_func
iteratenbem(tginst,iteratenbemargs)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 533, in iteratenbem
retlist=em_whileloop(sk,beta_init_mat,size_vec,wfrac_list,alpha_dispersion,alpha_val,estimateeff,updateeff,removeoutliers,debug)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 265, in em_whileloop
xwx_inv=linalg.inv(xwx_mat)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/linalg/basic.py", line 934, in inv
a1 = _asarray_validated(a, check_finite=check_finite)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/_lib/_util.py", line 262, in _asarray_validated
a = toarray(a)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/lib/function_base.py", line 485, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs
INFO @ Sat, 29 May 2021 19:54:23: Thread 0 completed.
INFO @ Sat, 29 May 2021 19:54:23: All threads completed.
INFO @ Sat, 29 May 2021 19:54:23: Using 200 genes and 200 sgRNAs as negative controls for permutation...
INFO @ Sat, 29 May 2021 19:54:23: Permuting groups of gene with 1 sgRNAs per gene. Group progress: 1/1
INFO @ Sat, 29 May 2021 19:54:23: Start permuting 2 rounds ...
INFO @ Sat, 29 May 2021 19:54:23: Collecting 200 sgRNAs from 200 genes.
INFO @ Sat, 29 May 2021 19:54:23: Permuting round 0 ...
INFO @ Sat, 29 May 2021 19:54:24: Thread 0 started.
INFO @ Sat, 29 May 2021 19:54:24: Thread 0: total 7637 instances.
/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:445: RuntimeWarning: Mean of empty slice.
return N.ndarray.mean(self, axis, dtype, out, keepdims=True)._collapse(axis)
/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/core/_methods.py:162: RuntimeWarning: invalid value encountered in true_divide
ret = um.true_divide(
Process Thread 0:
Traceback (most recent call last):
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, self._kwargs)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 38, in thread_p_func
iteratenbem(tginst,iteratenbemargs)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 533, in iteratenbem
retlist=em_whileloop(sk,beta_init_mat,size_vec,wfrac_list,alpha_dispersion,alpha_val,estimateeff,updateeff,removeoutliers,debug)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 265, in em_whileloop
xwx_inv=linalg.inv(xwx_mat)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/linalg/basic.py", line 934, in inv
a1 = _asarray_validated(a, check_finite=check_finite)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/_lib/_util.py", line 262, in _asarray_validated
a = toarray(a)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/lib/function_base.py", line 485, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs
INFO @ Sat, 29 May 2021 19:54:24: Thread 0 completed.
INFO @ Sat, 29 May 2021 19:54:24: All threads completed.
Traceback (most recent call last):
File "/backup/home/changxing/anaconda3/envs/MAGeCK/bin/mageck", line 66, in
main();
File "/backup/home/changxing/anaconda3/envs/MAGeCK/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemageck.py", line 218, in mageckmle_main
iteratenbem_permutation_by_nsg(allgenedict,args,size_f=size_f)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 278, in iteratenbem_permutation_by_nsg
last_permuted_beta=iteratenbem_permutation(this_genedict,args,sg_per_gene=ngene,background_genedict=bg_genedict,nround=args.permutation_round,allgenedict=genedict,removeoutliers=args.remove_outliers,size_factor=size_f)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 199, in iteratenbem_permutation
betazeros[betaz_id,:]=beta_es
ValueError: cannot copy sequence with size 0 to array axis with dimension 3
Error: mageck mle; how to solve this problem？
INFO @ Sat, 29 May 2021 19:54:23: Parameters: /backup/home/changxing/anaconda3/envs/MAGeCK/bin/mageck mle --count-table BatchCorrect.txt --design-matrix designmatrix.txt --norm-method control --control-sgrna ctrl_sgrna_list.txt --output-prefix braf.mle INFO @ Sat, 29 May 2021 19:54:23: Cannot parse design matrix as a string; try to parse it as a file name ... INFO @ Sat, 29 May 2021 19:54:23: Design matrix: INFO @ Sat, 29 May 2021 19:54:23: [[1. 1. 0. 0.] INFO @ Sat, 29 May 2021 19:54:23: [1. 1. 0. 0.] INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 1. 0.] INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 1. 0.] INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 0. 1.] INFO @ Sat, 29 May 2021 19:54:23: [1. 0. 0. 1.]] INFO @ Sat, 29 May 2021 19:54:23: Beta labels:baseline,Day4,Day10,Day18 INFO @ Sat, 29 May 2021 19:54:23: Included samples:sample1_1,sample2_1,sample1_2,sample2_2,sample1_3,sample2_3 INFO @ Sat, 29 May 2021 19:54:23: Loaded samples:sample1_1;sample2_1;sample1_2;sample2_2;sample1_3;sample2_3 INFO @ Sat, 29 May 2021 19:54:23: Sample index: 0;3;1;4;2;5 INFO @ Sat, 29 May 2021 19:54:23: Loaded 7637 genes. INFO @ Sat, 29 May 2021 19:54:23: 200 out of 200 control sgRNAs are found in count table. INFO @ Sat, 29 May 2021 19:54:23: Loaded 200 control sgRNAs from ctrl_sgrna_list.txt INFO @ Sat, 29 May 2021 19:54:23: control sgRNAs for normalization:200 INFO @ Sat, 29 May 2021 19:54:23: Final size factor: 0.7418480620804788 0.9801916242140984 1.22032074908657 1.3618267986174515 1.0019762721094752 0.7725871057326363 INFO @ Sat, 29 May 2021 19:54:23: size factor: 1.3479849191700333,1.020208676851104,0.8194566885374328,0.7343077702797567,0.9980276258385695,1.2943524329877476 INFO @ Sat, 29 May 2021 19:54:23: Thread 0 started. INFO @ Sat, 29 May 2021 19:54:23: Thread 0: total 1 instances. /backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:445: RuntimeWarning: Mean of empty slice. return N.ndarray.mean(self, axis, dtype, out, keepdims=True)._collapse(axis) /backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/core/_methods.py:162: RuntimeWarning: invalid value encountered in true_divide ret = um.true_divide( Process Thread 0: Traceback (most recent call last): File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 38, in thread_p_func iteratenbem(tginst,iteratenbemargs) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 533, in iteratenbem retlist=em_whileloop(sk,beta_init_mat,size_vec,wfrac_list,alpha_dispersion,alpha_val,estimateeff,updateeff,removeoutliers,debug) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 265, in em_whileloop xwx_inv=linalg.inv(xwx_mat) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/linalg/basic.py", line 934, in inv a1 = _asarray_validated(a, check_finite=check_finite) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/_lib/_util.py", line 262, in _asarray_validated a = toarray(a) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/lib/function_base.py", line 485, in asarray_chkfinite raise ValueError( ValueError: array must not contain infs or NaNs INFO @ Sat, 29 May 2021 19:54:23: Thread 0 completed. INFO @ Sat, 29 May 2021 19:54:23: All threads completed. INFO @ Sat, 29 May 2021 19:54:23: Modeling the mean and variance ... INFO @ Sat, 29 May 2021 19:54:23: Run the algorithm for the second time ... INFO @ Sat, 29 May 2021 19:54:23: Thread 0 started. INFO @ Sat, 29 May 2021 19:54:23: Thread 0: total 7637 instances. /backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:445: RuntimeWarning: Mean of empty slice. return N.ndarray.mean(self, axis, dtype, out, keepdims=True)._collapse(axis) /backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/core/_methods.py:162: RuntimeWarning: invalid value encountered in true_divide ret = um.true_divide( Process Thread 0: Traceback (most recent call last): File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(self._args, self._kwargs) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 38, in thread_p_func iteratenbem(tginst,iteratenbemargs) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 533, in iteratenbem retlist=em_whileloop(sk,beta_init_mat,size_vec,wfrac_list,alpha_dispersion,alpha_val,estimateeff,updateeff,removeoutliers,debug) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 265, in em_whileloop xwx_inv=linalg.inv(xwx_mat) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/linalg/basic.py", line 934, in inv a1 = _asarray_validated(a, check_finite=check_finite) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/_lib/_util.py", line 262, in _asarray_validated a = toarray(a) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/lib/function_base.py", line 485, in asarray_chkfinite raise ValueError( ValueError: array must not contain infs or NaNs INFO @ Sat, 29 May 2021 19:54:23: Thread 0 completed. INFO @ Sat, 29 May 2021 19:54:23: All threads completed. INFO @ Sat, 29 May 2021 19:54:23: Using 200 genes and 200 sgRNAs as negative controls for permutation... INFO @ Sat, 29 May 2021 19:54:23: Permuting groups of gene with 1 sgRNAs per gene. Group progress: 1/1 INFO @ Sat, 29 May 2021 19:54:23: Start permuting 2 rounds ... INFO @ Sat, 29 May 2021 19:54:23: Collecting 200 sgRNAs from 200 genes. INFO @ Sat, 29 May 2021 19:54:23: Permuting round 0 ... INFO @ Sat, 29 May 2021 19:54:24: Thread 0 started. INFO @ Sat, 29 May 2021 19:54:24: Thread 0: total 7637 instances. /backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/matrixlib/defmatrix.py:445: RuntimeWarning: Mean of empty slice. return N.ndarray.mean(self, axis, dtype, out, keepdims=True)._collapse(axis) /backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/core/_methods.py:162: RuntimeWarning: invalid value encountered in true_divide ret = um.true_divide( Process Thread 0: Traceback (most recent call last): File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 38, in thread_p_func iteratenbem(tginst,iteratenbemargs) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 533, in iteratenbem retlist=em_whileloop(sk,beta_init_mat,size_vec,wfrac_list,alpha_dispersion,alpha_val,estimateeff,updateeff,removeoutliers,debug) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mleem.py", line 265, in em_whileloop xwx_inv=linalg.inv(xwx_mat) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/linalg/basic.py", line 934, in inv a1 = _asarray_validated(a, check_finite=check_finite) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/scipy/_lib/_util.py", line 262, in _asarray_validated a = toarray(a) File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/numpy/lib/function_base.py", line 485, in asarray_chkfinite raise ValueError( ValueError: array must not contain infs or NaNs INFO @ Sat, 29 May 2021 19:54:24: Thread 0 completed. INFO @ Sat, 29 May 2021 19:54:24: All threads completed. Traceback (most recent call last): File "/backup/home/changxing/anaconda3/envs/MAGeCK/bin/mageck", line 66, in
main();
File "/backup/home/changxing/anaconda3/envs/MAGeCK/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemageck.py", line 218, in mageckmle_main
iteratenbem_permutation_by_nsg(allgenedict,args,size_f=size_f)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 278, in iteratenbem_permutation_by_nsg
last_permuted_beta=iteratenbem_permutation(this_genedict,args,sg_per_gene=ngene,background_genedict=bg_genedict,nround=args.permutation_round,allgenedict=genedict,removeoutliers=args.remove_outliers,size_factor=size_f)
File "/backup/home/changxing/anaconda3/envs/MAGeCK/lib/python3.8/site-packages/mageck/mlemultiprocessing.py", line 199, in iteratenbem_permutation
betazeros[betaz_id,:]=beta_es
ValueError: cannot copy sequence with size 0 to array axis with dimension 3