jts
commented
6 years ago Hi Sam,
This repository is for reproducing the results in our paper. If you want to use our methylation calling tool it is located here:
github.com/jts/nanopolish
There is a tutorial describing how to use it here:
http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html
Jared
On Thu, Mar 22, 2018 at 9:53 PM, Sam notifications@github.com wrote:
Hi
It seems very interesting tool. I like to use this to for methylation analysis on my data. however, I am getting an error while setting up the pipeline.
when I run pipeline.make after few minutes I'm getting this error.
Since I'm not an admin, I have installed dependencies like HDF5 using anaconda cloud. I wonder I can use those paths to this program.
Also, how can I input my own data? which file I should modify?
Sorry for asking too many questions at once.
. . .
HEAD is now at 4533516... don't try to replace the ONT model for R7 data Makefile💯 .depend: No such file or directory make: Warning: File `Makefile' has modification time 4.6e+03 s in the future wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/ src/hdf5-1.8.14.tar.gz --2018-03-22 18:34:29-- https://support.hdfgroup.org/ ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.t ar.gz Resolving support.hdfgroup.org... 50.28.50.143 Connecting to support.hdfgroup.org|50.28.50.143|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2018-03-22 18:34:30 ERROR 404: Not Found.
make: *** [lib/libhdf5.a] Error 8 ./pipeline.make: line 56: -cd: command not found ./pipeline.make: line 56: ../: Is a directory ./pipeline.make: line 72: .DEFAULT_GOAL: command not found ./pipeline.make: line 73: all:: command not found ./pipeline.make: line 74: all-except-cancer-normal:: command not found ./pipeline.make: line 76: all-software:: command not found ./pipeline.make: line 77: BISULFITE_BED: command not found ./pipeline.make: line 77: HUMAN_REFERENCE: command not found ./pipeline.make: line 77: ECOLI_REFERENCE: command not found ./pipeline.make: line 77: all-download:: command not found ./pipeline.make: line 81: 2: command not found ./pipeline.make: command substitution: line 82: syntax error near unexpected token )' ./pipeline.make: command substitution: line 82:if $(findstring $(1),$(v)),,$(v))' ./pipeline.make: line 81: FILTER_OUT: command not found ./pipeline.make: line 83: 2: command not found ./pipeline.make: command substitution: line 84: syntax error near unexpected token )' ./pipeline.make: command substitution: line 84:if $(findstring $(1),$(v)),$(v),)' ./pipeline.make: line 83: FILTER_IN: command not found ./pipeline.make: line 88: DATA_ROOT: command not found ./pipeline.make: line 88: wildcard: command not found ./pipeline.make: line 88: patsubst: command not found ./pipeline.make: line 88: notdir: command not found ./pipeline.make: line 88: NA12878.native.merged.fasta: command not found ./pipeline.make: line 90: DATA_ROOT: command not found ./pipeline.make: line 90: wildcard: command not found ./pipeline.make: line 90: patsubst: command not found ./pipeline.make: line 90: notdir: command not found ./pipeline.make: line 91: mcf10a.rr2.timp.031116.fasta: command not found ./pipeline.make: line 95: all_ecoli: command not found ./pipeline.make: line 95: patsubst: command not found ./pipeline.make: line 95: all-nucleotide:: command not found ./pipeline.make: line 96: all_ecoli: command not found ./pipeline.make: line 96: patsubst: command not found ./pipeline.make: line 96: all-cpg:: command not found ./pipeline.make: line 99: all_NA12878: command not found ./pipeline.make: line 99: patsubst: command not found ./pipeline.make: line 99: addprefix: command not found ./pipeline.make: line 99: all-island-plots:: command not found ./pipeline.make: line 101: all-training-plots:: command not found ./pipeline.make: line 103: all-accuracy-plots:: command not found ./pipeline.make: line 105: all-TSS-plots:: command not found ./pipeline.make: line 107: all-results-plots:: command not found ./pipeline.make: line 109: all-cancer-normal:: command not found ./pipeline.make: line 160: all_ecoli: command not found Usage: file [-bchikLNnprsvz0] [--apple] [--mime-encoding] [--mime-type] [-e testname] [-F separator] [-f namefile] [-m magicfiles] file ... file -C [-m magicfiles] file [--help] ./pipeline.make: line 160: ECOLI_REFERENCE: command not found ./pipeline.make: line 160: foreach: command not found ./pipeline.make: line 163: all_NA12878: command not found Usage: file [-bchikLNnprsvz0] [--apple] [--mime-encoding] [--mime-type] [-e testname] [-F separator] [-f namefile] [-m magicfiles] file ... file -C [-m magicfiles] file [--help] ./pipeline.make: line 163: HUMAN_REFERENCE: command not found ./pipeline.make: line 163: foreach: command not found ./pipeline.make: line 166: all_cancer: command not found Usage: file [-bchikLNnprsvz0] [--apple] [--mime-encoding] [--mime-type] [-e testname] [-F separator] [-f namefile] [-m magicfiles] file ... file -C [-m magicfiles] file [--help] ./pipeline.make: line 166: HUMAN_REFERENCE: command not found ./pipeline.make: line 166: foreach: command not found ./pipeline.make: line 171: ECOLI_REFERENCE: command not found ./pipeline.make: line 175: METHYLTRAIN_EXTRA_OPTS: command not found ./pipeline.make: line 192: ECOLI_REFERENCE: command not found ./pipeline.make: line 193: $@: ambiguous redirect % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 1408k 0 4344 0 0 1646 0 0:14:35 0:00:02 0:14:33 16643 curl: (23) Failed writing body (1200 != 1448) ./pipeline.make: line 195: HUMAN_REFERENCE: command not found ./pipeline.make: line 196: $@: ambiguous redirect % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 805M 0 4344 0 0 1796 0 5d 10h 0:00:02 5d 10h 16029 curl: (23) Failed writing body (1200 != 1448) ./pipeline.make: line 203: DATA_ROOT: command not found ./pipeline.make: line 203: fg: no job control ./pipeline.make: line 204: syntax error near unexpected token >' ./pipeline.make: line 204: $(PORETOOLS) fasta --type 2D $< > $@'
Thanks in advance Sam
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Hi
It seems very interesting tool. I like to use this to for methylation analysis on my data. however, I am getting an error while setting up the pipeline.
when I run pipeline.make after few minutes I'm getting this error.
Since I'm not an admin, I have installed dependencies like HDF5 using anaconda cloud. I wonder I can use those paths to this program.
Also, how can I input my own data? which file I should modify?
Sorry for asking too many questions at once.
. . .
HEAD is now at 4533516... don't try to replace the ONT model for R7 data Makefile:100: .depend: No such file or directory make: Warning: File `Makefile' has modification time 4.6e+03 s in the future wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz --2018-03-22 18:34:29-- https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.t ar.gz Resolving support.hdfgroup.org... 50.28.50.143 Connecting to support.hdfgroup.org|50.28.50.143|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2018-03-22 18:34:30 ERROR 404: Not Found.
make: *** [lib/libhdf5.a] Error 8 ./pipeline.make: line 56: -cd: command not found ./pipeline.make: line 56: ../: Is a directory ./pipeline.make: line 72: .DEFAULT_GOAL: command not found ./pipeline.make: line 73: all:: command not found ./pipeline.make: line 74: all-except-cancer-normal:: command not found ./pipeline.make: line 76: all-software:: command not found ./pipeline.make: line 77: BISULFITE_BED: command not found ./pipeline.make: line 77: HUMAN_REFERENCE: command not found ./pipeline.make: line 77: ECOLI_REFERENCE: command not found ./pipeline.make: line 77: all-download:: command not found ./pipeline.make: line 81: 2: command not found ./pipeline.make: command substitution: line 82: syntax error near unexpected token
)' ./pipeline.make: command substitution: line 82:if $(findstring $(1),$(v)),,$(v))' ./pipeline.make: line 81: FILTER_OUT: command not found ./pipeline.make: line 83: 2: command not found ./pipeline.make: command substitution: line 84: syntax error near unexpected token)' ./pipeline.make: command substitution: line 84:if $(findstring $(1),$(v)),$(v),)' ./pipeline.make: line 83: FILTER_IN: command not found ./pipeline.make: line 88: DATA_ROOT: command not found ./pipeline.make: line 88: wildcard: command not found ./pipeline.make: line 88: patsubst: command not found ./pipeline.make: line 88: notdir: command not found ./pipeline.make: line 88: NA12878.native.merged.fasta: command not found ./pipeline.make: line 90: DATA_ROOT: command not found ./pipeline.make: line 90: wildcard: command not found ./pipeline.make: line 90: patsubst: command not found ./pipeline.make: line 90: notdir: command not found ./pipeline.make: line 91: mcf10a.rr2.timp.031116.fasta: command not found ./pipeline.make: line 95: all_ecoli: command not found ./pipeline.make: line 95: patsubst: command not found ./pipeline.make: line 95: all-nucleotide:: command not found ./pipeline.make: line 96: all_ecoli: command not found ./pipeline.make: line 96: patsubst: command not found ./pipeline.make: line 96: all-cpg:: command not found ./pipeline.make: line 99: all_NA12878: command not found ./pipeline.make: line 99: patsubst: command not found ./pipeline.make: line 99: addprefix: command not found ./pipeline.make: line 99: all-island-plots:: command not found ./pipeline.make: line 101: all-training-plots:: command not found ./pipeline.make: line 103: all-accuracy-plots:: command not found ./pipeline.make: line 105: all-TSS-plots:: command not found ./pipeline.make: line 107: all-results-plots:: command not found ./pipeline.make: line 109: all-cancer-normal:: command not found ./pipeline.make: line 160: all_ecoli: command not found Usage: file [-bchikLNnprsvz0] [--apple] [--mime-encoding] [--mime-type] [-e testname] [-F separator] [-f namefile] [-m magicfiles] file ... file -C [-m magicfiles] file [--help] ./pipeline.make: line 160: ECOLI_REFERENCE: command not found ./pipeline.make: line 160: foreach: command not found ./pipeline.make: line 163: all_NA12878: command not found Usage: file [-bchikLNnprsvz0] [--apple] [--mime-encoding] [--mime-type] [-e testname] [-F separator] [-f namefile] [-m magicfiles] file ... file -C [-m magicfiles] file [--help] ./pipeline.make: line 163: HUMAN_REFERENCE: command not found ./pipeline.make: line 163: foreach: command not found ./pipeline.make: line 166: all_cancer: command not found Usage: file [-bchikLNnprsvz0] [--apple] [--mime-encoding] [--mime-type] [-e testname] [-F separator] [-f namefile] [-m magicfiles] file ... file -C [-m magicfiles] file [--help] ./pipeline.make: line 166: HUMAN_REFERENCE: command not found ./pipeline.make: line 166: foreach: command not found ./pipeline.make: line 171: ECOLI_REFERENCE: command not found ./pipeline.make: line 175: METHYLTRAIN_EXTRA_OPTS: command not found ./pipeline.make: line 192: ECOLI_REFERENCE: command not found ./pipeline.make: line 193: $@: ambiguous redirect % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 1408k 0 4344 0 0 1646 0 0:14:35 0:00:02 0:14:33 16643 curl: (23) Failed writing body (1200 != 1448) ./pipeline.make: line 195: HUMAN_REFERENCE: command not found ./pipeline.make: line 196: $@: ambiguous redirect % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 805M 0 4344 0 0 1796 0 5d 10h 0:00:02 5d 10h 16029 curl: (23) Failed writing body (1200 != 1448) ./pipeline.make: line 203: DATA_ROOT: command not found ./pipeline.make: line 203: fg: no job control ./pipeline.make: line 204: syntax error near unexpected token>' ./pipeline.make: line 204:$(PORETOOLS) fasta --type 2D $< > $@'Thanks in advance Sam