r3fang
commented
4 years ago can you test if MACS has been successfully installed by running this command “./dir/macs2”, what is the outcome of this command?
-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego
On Oct 1, 2019, at 5:15 PM, kchowdhary4 notifications@github.com wrote:
Hi, I've trying to run the runMACS command in order to call peaks on my clusters. However, I keep running into problems with there not being snaptools.parser available or problems importing the correct numpy multiarray_umath.
Here is my code :
clusters.sel = names(table(x.sp@cluster))[which(table(x.sp@cluster) > 100)]; peaks.ls = mclapply(seq(clusters.sel), function(i){ print(clusters.sel[i]); runMACS( obj=x.sp[which(x.sp@cluster==clusters.sel[i]),], output.prefix=paste0("teffatac.", gsub(" ", "", clusters.sel)[i]), path.to.snaptools="/anaconda/envs/py3/bin/snaptools", path.to.macs="/anaconda/envs/py3/bin/macs2", gsize="mm", # mm, hs, etc buffer.size=500, num.cores=1, macs.options="--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits", tmp.folder=tempdir() ); }, mc.cores=1);
Here is the output I get:
`Epoch: checking input parameters ... Epoch: extracting fragments from each snap files ... Traceback (most recent call last): File "/anaconda/envs/py3/bin/snaptools", line 36, in from snaptools.parser import parse_args ImportError: No module named snaptools.parser cat: /var/folders/vc/k9mh38dn1_5bslrm1ztjwlz00000gn/T//RtmpUArhVg/filef105a1f7b40.bed.gz: No such file or directory Traceback (most recent call last): File "/anaconda/envs/py3/bin/macs2", line 650, in main() File "/anaconda/envs/py3/bin/macs2", line 48, in main from MACS2.callpeak_cmd import run File "/anaconda/envs/py3/lib/python2.7/site-packages/MACS2/callpeak_cmd.py", line 23, in from MACS2.OptValidator import opt_validate File "/anaconda/envs/py3/lib/python2.7/site-packages/MACS2/OptValidator.py", line 20, in from MACS2.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, File "init.pxd", line 206, in init MACS2.IO.Parser File "/anaconda/envs/py3/lib/python2.7/site-packages/numpy/init.py", line 142, in from . import core File "/anaconda/envs/py3/lib/python2.7/site-packages/numpy/core/init.py", line 71, in raise ImportError(msg) ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. Here is how to proceed:
If you're working with a numpy git repository, try git clean -xdf (removes all files not under version control) and rebuild numpy. If you are simply trying to use the numpy version that you have installed: your installation is broken - please reinstall numpy. If you have already reinstalled and that did not fix the problem, then: Check that you are using the Python you expect (you're using /anaconda/envs/py3/bin/python), and that you have no directories in your PATH or PYTHONPATH that can interfere with the Python and numpy versions you're trying to use.
If (1) looks fine, you can open a new issue at https://github.com/numpy/numpy/issues https://github.com/numpy/numpy/issues. Please include details on:
how you installed Python how you installed numpy your operating system whether or not you have multiple versions of Python installed if you built from source, your compiler versions and ideally a build log Note: this error has many possible causes, so please don't comment on an existing issue about this - open a new one instead.
Original error was: dlopen(/anaconda/envs/py3/lib/python2.7/site-packages/numpy/core/_multiarray_umath.so, 2): Library not loaded: @rpath/libopenblas.dylib Referenced from: /anaconda/envs/py3/lib/python2.7/site-packages/numpy/core/_multiarray_umath.so Reason: image not found
Error in runMACS(obj = x.sp[which(x.sp@cluster == clusters.sel[i]), ], : 'MACS' call failed`
I've tried everything from changing my python environments, reinstalling snaptools/numpy/macs2, etc.
Any help on this would be very much appreciated -- thank you!
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kchowdhary4
Hi, I've trying to run the runMACS command in order to call peaks on my clusters. However, I keep running into problems with there not being snaptools.parser available or problems importing the correct numpy multiarray_umath.
Here is my code :
`clusters.sel = names(table(x.sp@cluster))[which(table(x.sp@cluster) > 100)];
peaks.ls = mclapply(seq(clusters.sel), function(i){ print(clusters.sel[i]); runMACS( obj=x.sp[which(x.sp@cluster==clusters.sel[i]),], output.prefix=paste0("teffatac.", gsub(" ", "", clusters.sel)[i]), path.to.snaptools="/anaconda/envs/py3/bin/snaptools", path.to.macs="/anaconda/envs/py3/bin/macs2", gsize="mm", # mm, hs, etc buffer.size=500, num.cores=1, macs.options="--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits", tmp.folder=tempdir() ); }, mc.cores=1);`
Here is the output I get:
`Epoch: checking input parameters ... Epoch: extracting fragments from each snap files ... Traceback (most recent call last): File "/anaconda/envs/py3/bin/snaptools", line 36, in
from snaptools.parser import parse_args
ImportError: No module named snaptools.parser
cat: /var/folders/vc/k9mh38dn1_5bslrm1ztjwlz00000gn/T//RtmpUArhVg/filef105a1f7b40.bed.gz: No such file or directory
Traceback (most recent call last):
File "/anaconda/envs/py3/bin/macs2", line 650, in
main()
File "/anaconda/envs/py3/bin/macs2", line 48, in main
from MACS2.callpeak_cmd import run
File "/anaconda/envs/py3/lib/python2.7/site-packages/MACS2/callpeak_cmd.py", line 23, in
from MACS2.OptValidator import opt_validate
File "/anaconda/envs/py3/lib/python2.7/site-packages/MACS2/OptValidator.py", line 20, in
from MACS2.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, \
File "init.pxd", line 206, in init MACS2.IO.Parser
File "/anaconda/envs/py3/lib/python2.7/site-packages/numpy/init.py", line 142, in
from . import core
File "/anaconda/envs/py3/lib/python2.7/site-packages/numpy/core/init.py", line 71, in
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. Here is how to proceed:
git clean -xdf(removes all files not under version control) and rebuild numpy.If you have already reinstalled and that did not fix the problem, then:
If (1) looks fine, you can open a new issue at https://github.com/numpy/numpy/issues. Please include details on:
Note: this error has many possible causes, so please don't comment on an existing issue about this - open a new one instead.
Original error was: dlopen(/anaconda/envs/py3/lib/python2.7/site-packages/numpy/core/_multiarray_umath.so, 2): Library not loaded: @rpath/libopenblas.dylib Referenced from: /anaconda/envs/py3/lib/python2.7/site-packages/numpy/core/_multiarray_umath.so Reason: image not found
Error in runMACS(obj = x.sp[which(x.sp@cluster == clusters.sel[i]), ], : 'MACS' call failed`
I've tried everything from changing my python environments, reinstalling snaptools/numpy/macs2, etc.
Any help on this would be very much appreciated -- thank you!