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brentp / combined-pvalues

combining p-values using modified stouffer-liptak for spatially correlated results (probes)
MIT License
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ModuleNotFoundError: No module named '_common' #20

Closed Lei-Guo closed 4 years ago

Lei-Guo commented 4 years ago

comb-p pipeline -c 4 --dist 500 --step 60 --seed 0.01 file.bed

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.0', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.0-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.0-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.0-py3.7.egg/cpv/pipeline.py", line 9, in main from _common import get_col_num ModuleNotFoundError: No module named '_common'

brentp commented 4 years ago

thanks for reporting. i just pushed a fix for this.

Lei-Guo commented 4 years ago

Thank you for your quick response. Below are new errors. Did I not run it correctly?

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 1:50 PM Brent Pedersen notifications@github.com wrote:

thanks for reporting. i just pushed a fix for this.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/combined-pvalues/issues/20?email_source=notifications&email_token=ACSH7P75SRYX4UILJWINODLQZJWJDA5CNFSM4J4PDAF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHHDJCA#issuecomment-567161992, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSH7P3IXNZ2OPYGXSSMCN3QZJWJDANCNFSM4J4PDAFQ .

-- Gray

brentp commented 4 years ago

I made another change, can you pull from master, re-install, and try again?

Lei-Guo commented 4 years ago

I downloaded the updated version and the problem still persists.

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 3:14 PM Lei Guo grayapply2009@gmail.com wrote:

Thank you for your quick response. Below are new errors. Did I not run it correctly?

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 1:50 PM Brent Pedersen notifications@github.com wrote:

thanks for reporting. i just pushed a fix for this.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/combined-pvalues/issues/20?email_source=notifications&email_token=ACSH7P75SRYX4UILJWINODLQZJWJDA5CNFSM4J4PDAF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHHDJCA#issuecomment-567161992, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSH7P3IXNZ2OPYGXSSMCN3QZJWJDANCNFSM4J4PDAFQ .

-- Gray

-- Gray

Lei-Guo commented 4 years ago

Sorry, pasted wrong error message.

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Done with one-time ACF calculation

21789882 bases used as coverage for sidak correction wrote: fake.regions-p.bed.gz, (regions with corrected-p < 0.05: 32) /bin/bash: bedtools: command not found cmd was:bedtools intersect -b /tmp/tmpltzz5ln1 -a fake.regions-p.bed.gz -wo return code was:127 Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.3', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/cpv/pipeline.py", line 183, in pipeline regions_bed, p_col_name=col_num)): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/cpv/filter.py", line 95, in filter header=rh + ph), itemgetter('chrom','start','end')): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/toolshed-0.4.6-py3.7.egg/toolshed/files.py", line 278, in reader for toks in line_gen: File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/toolshed-0.4.6-py3.7.egg/toolshed/files.py", line 61, in process_iter raise ProcessException(cmd) toolshed.files.ProcessException: bedtools intersect -b /tmp/tmpltzz5ln1 -a fake.regions-p.bed.gz -wo

On Wed, Dec 18, 2019 at 3:40 PM Lei Guo grayapply2009@gmail.com wrote:

I downloaded the updated version and the problem still persists.

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 3:14 PM Lei Guo grayapply2009@gmail.com wrote:

Thank you for your quick response. Below are new errors. Did I not run it correctly?

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 1:50 PM Brent Pedersen notifications@github.com wrote:

thanks for reporting. i just pushed a fix for this.

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Lei-Guo commented 4 years ago

My bad, just forgot loading the bedtools

On Wed, Dec 18, 2019 at 3:44 PM Lei Guo grayapply2009@gmail.com wrote:

Sorry, pasted wrong error message.

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Done with one-time ACF calculation

21789882 bases used as coverage for sidak correction wrote: fake.regions-p.bed.gz, (regions with corrected-p < 0.05: 32) /bin/bash: bedtools: command not found cmd was:bedtools intersect -b /tmp/tmpltzz5ln1 -a fake.regions-p.bed.gz -wo return code was:127 Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.3', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/cpv/pipeline.py", line 183, in pipeline regions_bed, p_col_name=col_num)): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.3-py3.7.egg/cpv/filter.py", line 95, in filter header=rh + ph), itemgetter('chrom','start','end')): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/toolshed-0.4.6-py3.7.egg/toolshed/files.py", line 278, in reader for toks in line_gen: File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/toolshed-0.4.6-py3.7.egg/toolshed/files.py", line 61, in process_iter raise ProcessException(cmd) toolshed.files.ProcessException: bedtools intersect -b /tmp/tmpltzz5ln1 -a fake.regions-p.bed.gz -wo

On Wed, Dec 18, 2019 at 3:40 PM Lei Guo grayapply2009@gmail.com wrote:

I downloaded the updated version and the problem still persists.

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 3:14 PM Lei Guo grayapply2009@gmail.com wrote:

Thank you for your quick response. Below are new errors. Did I not run it correctly?

comb-p pipeline --seed 0.01 --dist 300 --step 300 pvalues.bed -p fake setting --acf-dist to 0.33 * --dist == 100 ACF:

lag_min lag_max correlation N p

1 301 0.05892 544300 0 wrote: fake.acf.txt

original lambda: 1.06

wrote: fake.slk.bed.gz with lambda: 1.04 wrote: fake.fdr.bed.gz wrote: fake.regions.bed.gz (73 regions)

read 73 regions from fake.regions.bed.gz

calculating ACF out to: 561

with 3 lags: [1, 301, 601]

Traceback (most recent call last): File "/hpc/users/guol03/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1462, in run_script exec(code, namespace, namespace) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 170, in pipeline step): File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 175, in region_p acfs = _gen_acf(region_info, (fpvals,), col_num, step) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/region_p.py", line 89, in _gen_acf acfs = acf(fpvals, lags, col_num, simple=True) File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/acf.py", line 88, in acf imap = get_map() File "/hpc/users/guol03/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 169, in get_map p = Pool(None, pool_sig) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 176, in init self._repopulate_pool() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/pool.py", line 241, in _repopulate_pool w.start() File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/process.py", line 112, in start self._popen = self._Popen(self) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/context.py", line 277, in _Popen return Popen(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init self._launch(process_obj) File "/hpc/users/guol03/anaconda3/lib/python3.7/multiprocessing/popen_fork.py", line 70, in _launch self.pid = os.fork() BlockingIOError: [Errno 11] Resource temporarily unavailable

On Wed, Dec 18, 2019 at 1:50 PM Brent Pedersen notifications@github.com wrote:

thanks for reporting. i just pushed a fix for this.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/combined-pvalues/issues/20?email_source=notifications&email_token=ACSH7P75SRYX4UILJWINODLQZJWJDA5CNFSM4J4PDAF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHHDJCA#issuecomment-567161992, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSH7P3IXNZ2OPYGXSSMCN3QZJWJDANCNFSM4J4PDAFQ .

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