simonvh
commented
2 years ago Hi Francesco, can provide the exact command-line you use to run gimme maelstrom, the full error message and if possible a sample of your input file that gives this error?
Closed Francis3209 closed 1 year ago
simonvh
commented
2 years ago Hi Francesco, can provide the exact command-line you use to run gimme maelstrom, the full error message and if possible a sample of your input file that gives this error?
Francis3209
commented
2 years ago Hi, yes, of course. This is my command line: gimme maelstrom ${output_folder}/${exp}.diffPeaksForMaelstrom.txt ${genomefile} ${output_folder}/${exp}.gimmeMaelstrom.results.txt
where $genomefile is /Users/ieoxxx/Work/genome_annotations/hg38/hg38.fa
Here's the full error message:
Fontconfig warning: ignoring UTF-8: not a valid region tag
2021-10-14 14:12:14,241 - INFO - Starting maelstrom
2021-10-14 14:12:14,624 - INFO - motif scanning (counts)
2021-10-14 14:12:14,624 - INFO - reading table
2021-10-14 14:12:17,564 - INFO - setting threshold
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Traceback (most recent call last):
File "
And the input txt file for the analysis.
Cfpac1.diffPeaksForMaelstrom.txt
Thank you!!
simonvh
commented
2 years ago I suspect it's this line in your input file:
chr22_KI270733v1_random:-142-358Can you try removing that and rerunning gimme maelstrom?
Francis3209
commented
2 years ago Yes, I removed the line and now it seems to work! thanks a lot!! Francesco
Francis3209
commented
2 years ago Hi Simon, just last minor issue related to the analysis. Finally I got all output files however the report.html file was missing. These are the messages I got during the analysis:
Fontconfig warning: ignoring UTF-8: not a valid region tag 2021-10-14 17:13:26,724 - INFO - Starting maelstrom 2021-10-14 17:13:27,099 - INFO - motif scanning (counts) 2021-10-14 17:13:27,099 - INFO - reading table 2021-10-14 17:13:30,061 - INFO - setting threshold Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag Fontconfig warning: ignoring UTF-8: not a valid region tag 2021-10-14 17:13:39,998 - INFO - creating count table 2021-10-14 17:25:45,860 - INFO - done 2021-10-14 17:25:47,887 - INFO - creating dataframe 2021-10-14 17:26:36,577 - INFO - motif scanning (scores) 2021-10-14 17:26:36,579 - INFO - reading table 2021-10-14 17:26:44,066 - INFO - creating score table (z-score, GC%) Fontconfig warning: ignoring UTF-8: not a valid region tag
2021-10-14 17:57:45,926 - INFO - done 2021-10-14 17:57:46,644 - INFO - creating dataframe
2021-10-14 18:05:38,493 - INFO - Selecting non-redundant motifs
2021-10-14 18:09:53,567 - INFO - Selected 722 motifs
2021-10-14 18:09:53,567 - INFO - Motifs: /Users/ieo5634/Work/IEO/Projects/Pancreas/Alice/Cfpac1_h3k27ac_chip/motif_analysis/Maelstrom/Cfpac1.gimmeMaelstrom.results.txt/nonredundant.motifs.pfm
2021-10-14 18:09:53,567 - INFO - Factor mappings: /Users/ieo5634/Work/IEO/Projects/Pancreas/Alice/Cfpac1_h3k27ac_chip/motif_analysis/Maelstrom/Cfpac1.gimmeMaelstrom.results.txt/nonredundant.motifs.motif2factors.txt
2021-10-14 18:09:58,900 - INFO - Fitting BayesianRidge
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:44<00:00, 11.14s/it]
2021-10-14 18:10:44,677 - INFO - Done
2021-10-14 18:10:50,173 - INFO - Fitting XGBoostRegression
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [08:24<00:00, 126.20s/it]
2021-10-14 18:19:16,125 - INFO - Done
2021-10-14 18:19:21,626 - INFO - Fitting MultiTaskLasso
2021-10-14 21:14:51,011 - INFO - Done
2021-10-14 21:14:56,491 - INFO - Fitting SVR
2021-10-14 21:20:49,203 - INFO - Done
2021-10-14 21:20:49,243 - INFO - Rank aggregation
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
2021-10-14 21:20:58,616 - INFO - Correlation
2021-10-14 21:21:34,768 - INFO - html report
Traceback (most recent call last):
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/bin/gimme", line 11, in
Maybe something related to the report.py script? Thank you so much Francesco
simonvh
commented
2 years ago Hi Francesco, this is a strange bug that we still need to track down (it only occurs sporadically). If you rerun, it will likely be gone.
Francis3209
commented
2 years ago Hi Simon, ok thanks a lot for the help!
Francis3209
commented
2 years ago Hi Simon, Sorry for the further message but now I would need to run maelstrom using my custom .pfm motif file, the file I prepared seems to be formatted properly however when I run the program the following error message (at the bottom) appears:
Fontconfig warning: ignoring UTF-8: not a valid region tag
2021-10-25 16:42:36,567 - INFO - Starting maelstrom
2021-10-25 16:42:36,943 - INFO - motif scanning (counts)
2021-10-25 16:42:36,943 - INFO - reading table
2021-10-25 16:42:40,582 - INFO - setting threshold
2021-10-25 16:42:43,934 - INFO - determining FPR-based threshold
2021-10-25 16:48:11,565 - INFO - creating count table
Traceback (most recent call last):
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/bin/gimme", line 11, in
Here's my .pfm file used for the analysis.
Thanks a lot in case you have some suggestion. Best, Francesco 20170320_pwms_selected.pfm.txt
simonvh
commented
2 years ago Can you try replacing the whitespace (tabs) in the ID lines? I suspect this may cause an issue?
Francis3209
commented
2 years ago Hi Simon,
thank you for the message. I checked the whitespace and tabs in the headers of the pfm file and all seems ok, however this time I generated a new .pfm file starting from my custom motif file in jaspar, using the gimme motifs API for the format conversion. The file seems ok and I also prepared the correspoding .motif2factors.txt file, however, another strange error occurs when I launch maelstrom,
Fontconfig warning: ignoring UTF-8: not a valid region tag
2021-11-04 11:11:58,287 - INFO - Starting maelstrom
2021-11-04 11:11:58,656 - INFO - motif scanning (counts)
2021-11-04 11:11:58,656 - INFO - reading table
2021-11-04 11:12:02,025 - INFO - setting threshold
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Fontconfig warning: ignoring UTF-8: not a valid region tag
Traceback (most recent call last):
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/bin/gimme", line 11, in
Do you know a possible cause for this kind of error message ? Thanks a lot for all the help!
simonvh
commented
2 years ago Sorry, I seem to have missed this. Can you try removing the Gimmemotifs cache directory? Should be somewhere like ~/.cache/gimmemotifs
Francis3209
commented
2 years ago Hi Simon, ok, I try and let you know, thank you again!! Francesco
Francis3209
commented
2 years ago Hi, yes I confirm now it works! Just to remember to myself to remove the cache folder after each run. Thank you so much!
Hi Simon! I'm Francesco. I'm really enthusiastic about using your gimme motif suite to perform differential motif enrichment analysis. When I try with Maelstrom, however, I always received this error message that is very complex for me to solve.
Traceback (most recent call last): File "", line 1, in
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/multiprocessing/spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/multiprocessing/spawn.py", line 125, in _main
prepare(preparation_data)
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/multiprocessing/spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/runpy.py", line 268, in run_path
return _run_module_code(code, init_globals, run_name,
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/bin/gimme", line 8, in
from gimmemotifs.cli import cli
File "/Users/ieo5634/opt/anaconda3/envs/gimmeMotif/lib/python3.9/site-packages/gimmemotifs/init.py", line 61, in
from . import denovo
..... and at the bottom of the message this:
ValueError: invalid literal for int() with base 10: ''
As you suggested, I already tried to delete the gimme motif configuration file ~/.config/gimmemotifs/gimmemotifs.cfg and run it without any parameters, then run again my analysis but the problem remains.
I run the program on my Mac OS bigSur 11.5.2, these are my python and other packages versions:
_py-xgboost-mutex 2.0 cpu_0 conda-forge abseil-cpp 20210324.1 he49afe7_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge arrow-cpp 4.0.1 py39hc705ef8_0_cpu conda-forge aws-c-cal 0.5.9 h0df4f8a_0 conda-forge aws-c-common 0.5.11 h0d85af4_0 conda-forge aws-c-event-stream 0.2.7 h5ecfe7a_7 conda-forge aws-c-io 0.9.14 h9daffe9_1 conda-forge aws-checksums 0.1.11 h9daffe9_6 conda-forge aws-sdk-cpp 1.8.186 h8d473ab_2 conda-forge bedtools 2.30.0 haa7f73a_1 bioconda biofluff 3.0.4 py_0 bioconda biopython 1.78 py39h89e85a6_2 conda-forge boltons 21.0.0 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h046ec9c_4 conda-forge brotlipy 0.7.0 py39hcbf5805_1001 conda-forge bucketcache 0.12.1 py39hde42818_2 conda-forge bzip2 1.0.8 h0d85af4_4 conda-forge c-ares 1.17.1 h0d85af4_1 conda-forge ca-certificates 2021.5.30 h033912b_0 conda-forge certifi 2021.5.30 py39h6e9494a_0 conda-forge cffi 1.14.5 py39h319c39b_0 conda-forge chardet 4.0.0 py39h6e9494a_1 conda-forge click 8.0.1 py39h6e9494a_0 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge configparser 5.0.2 pyhd8ed1ab_0 conda-forge cryptography 3.4.7 py39ha2c9959_0 conda-forge cycler 0.10.0 py_2 conda-forge decorator 5.0.9 pyhd8ed1ab_0 conda-forge diskcache 5.2.1 pyh44b312d_0 conda-forge expat 2.2.10 h1c7c35f_0 conda-forge feather-format 0.4.1 pyh9f0ad1d_0 conda-forge freetype 2.10.4 h4cff582_1 conda-forge future 0.18.2 py39h6e9494a_3 conda-forge gadem 1.3.1 hb4d813b_3 bioconda genomepy 0.9.3 py_0 bioconda gflags 2.2.2 hb1e8313_1004 conda-forge ghostscript 9.54.0 he49afe7_1 conda-forge gimmemotifs 0.16.0 py39he2a1a62_2 bioconda glog 0.5.0 h25b26a9_0 conda-forge grpc-cpp 1.38.0 h25f885f_0 conda-forge homer 4.10 pl526h770b8ee_0 bioconda htseq 0.13.5 py39hdd6a155_1 bioconda htslib 1.12 hc38c3fb_1 bioconda icu 68.1 h74dc148_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge jbig 2.1 h0d85af4_2003 conda-forge jinja2 3.0.1 pyhd8ed1ab_0 conda-forge joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9d hbcb3906_0 conda-forge kiwisolver 1.3.1 py39hedf5dff_1 conda-forge krb5 1.19.1 hcfbf3a7_0 conda-forge lcms2 2.12 h577c468_0 conda-forge lerc 2.2.1 h046ec9c_0 conda-forge libblas 3.9.0 9_openblas conda-forge libcblas 3.9.0 9_openblas conda-forge libcurl 7.77.0 hf45b732_0 conda-forge libcxx 11.1.0 habf9029_0 conda-forge libdeflate 1.7 h35c211d_5 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libev 4.33 haf1e3a3_1 conda-forge libevent 2.1.10 hddc9c9b_3 conda-forge libffi 3.3 h046ec9c_2 conda-forge libgcc 4.8.5 1 conda-forge libgfortran 5.0.0 9_3_0_h6c81a4c_22 conda-forge libgfortran5 9.3.0 h6c81a4c_22 conda-forge libiconv 1.16 haf1e3a3_0 conda-forge liblapack 3.9.0 9_openblas conda-forge libllvm10 10.0.1 h009f743_3 conda-forge libnghttp2 1.43.0 h07e645a_0 conda-forge libopenblas 0.3.15 openmp_h5e1b9a4_1 conda-forge libpng 1.6.37 h7cec526_2 conda-forge libprotobuf 3.16.0 hcf210ce_0 conda-forge libssh2 1.9.0 h52ee1ee_6 conda-forge libthrift 0.14.1 hab56fdc_1 conda-forge libtiff 4.3.0 h1167814_1 conda-forge libutf8proc 2.6.1 h35c211d_0 conda-forge libuuid 2.32.1 h35c211d_1000 conda-forge libwebp-base 1.2.0 h0d85af4_2 conda-forge libxgboost 1.4.0 he49afe7_0 conda-forge libxml2 2.9.12 h93ec3fd_0 conda-forge libxslt 1.1.33 h5739fc3_2 conda-forge llvm-openmp 11.1.0 hda6cdc1_1 conda-forge llvmlite 0.36.0 py39h798a4f4_0 conda-forge logbook 1.5.3 py39hcbf5805_4 conda-forge logomaker 0.8 pyh864c0ab_1 bioconda loguru 0.5.3 py39h6e9494a_2 conda-forge lz4-c 1.9.3 h046ec9c_0 conda-forge markupsafe 2.0.1 py39h89e85a6_0 conda-forge matplotlib 3.4.2 py39h6e9494a_0 conda-forge matplotlib-base 3.4.2 py39hb07454d_0 conda-forge meme 5.3.0 py39pl5262hd110924_2 bioconda mpi 1.0 openmpi conda-forge mysql-connector-c 6.1.11 h0f02589_1007 conda-forge ncurses 6.2 h2e338ed_4 conda-forge norns 0.1.5 pyh864c0ab_1 bioconda nose 1.3.7 py_1006 conda-forge numba 0.53.1 py39he2616bd_0 conda-forge numpy 1.20.3 py39h7eed0ac_1 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjdk 11.0.9.1 hcf210ce_1 conda-forge openjpeg 2.4.0 h6e7aa92_1 conda-forge openmpi 4.1.1 hd3cd54c_0 conda-forge openssl 1.1.1k h0d85af4_0 conda-forge orc 1.6.8 hfe4c36d_0 conda-forge palettable 3.3.0 py_0 conda-forge pandas 1.2.4 py39h4d6be9b_0 conda-forge parquet-cpp 1.5.1 2 conda-forge pathlib 1.0.1 py39h6e9494a_4 conda-forge patsy 0.5.1 py_0 conda-forge perl 5.26.2 hbcb3906_1008 conda-forge perl-algorithm-cluster 1.58 pl526h1de35cc_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-cgi 4.40 pl526h470a237_0 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-constant 1.33 pl526_1 bioconda perl-dbi 1.642 pl526_0 bioconda perl-exporter 5.72 pl526_1 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-which 1.23 pl526_0 bioconda perl-html-parser 3.72 pl526h04f5b5a_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-template 2.97 pl526_1 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h04f5b5a_3 bioconda perl-log-log4perl 1.49 pl526_0 bioconda perl-math-cdf 0.1 pl526h1de35cc_5 bioconda perl-scalar-list-utils 1.52 pl526h01d97ff_0 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526hb1d6bea_1002 conda-forge perl-xml-sax 0.99 pl526_1 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xml-sax-expat 0.51 pl526_3 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xsloader 0.24 pl526_0 bioconda perl-yaml 1.29 pl526_0 bioconda pillow 8.2.0 py39h5fdd921_1 conda-forge pip 21.1.2 pyhd8ed1ab_0 conda-forge prosampler 1.0 h770b8ee_0 bioconda py-xgboost 1.4.0 py39h6e9494a_0 conda-forge pyarrow 4.0.1 py39hc3b5b9c_0_cpu conda-forge pybedtools 0.8.2 py39h33336d3_1 bioconda pybigwig 0.3.18 py39h8b2de0f_1 bioconda pycparser 2.20 pyh9f0ad1d_2 conda-forge pyfaidx 0.5.9.5 pyh3252c3a_0 bioconda pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pysam 0.16.0.1 py39h56703ae_3 bioconda pysocks 1.7.1 py39h6e9494a_3 conda-forge python 3.9.4 h9133fd0_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-xxhash 2.0.2 py39h89e85a6_0 conda-forge python_abi 3.9 1_cp39 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py39hcbf5805_0 conda-forge qnorm 0.7.0 pyh44b312d_0 conda-forge re2 2021.04.01 he49afe7_0 conda-forge readline 8.1 h05e3726_0 conda-forge represent 1.6.0 py39hb5aae12_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge scikit-learn 0.24.2 py39h4b1dcc9_0 conda-forge scipy 1.6.3 py39h056f1c0_0 conda-forge seaborn 0.11.1 hd8ed1ab_1 conda-forge seaborn-base 0.11.1 pyhd8ed1ab_1 conda-forge setuptools 49.6.0 py39h6e9494a_3 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.8 hb1e8313_3 conda-forge sqlite 3.35.5 h44b9ce1_0 conda-forge statsmodels 0.12.2 py39h329c335_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h0419947_1 conda-forge tornado 6.1 py39hcbf5805_1 conda-forge tqdm 4.61.0 pyhd8ed1ab_0 conda-forge trawler 2.0 hdfd78af_4 bioconda tzdata 2021a he74cb21_0 conda-forge ucsc-bedtogenepred 377 h516baf0_1 bioconda ucsc-bigbedtobed 377 h516baf0_1 bioconda ucsc-genepredtobed 377 h516baf0_3 bioconda ucsc-genepredtogtf 377 h516baf0_3 bioconda ucsc-gff3togenepred 377 h516baf0_1 bioconda ucsc-gtftogenepred 377 h516baf0_3 bioconda urllib3 1.26.5 pyhd8ed1ab_0 conda-forge weeder 2.0 hb280591_5 bioconda wheel 0.36.2 pyhd3deb0d_0 conda-forge xdg 5.0.2 pyhd8ed1ab_0 conda-forge xgboost 1.4.0 py39h6e9494a_0 conda-forge xmltodict 0.12.0 py_0 conda-forge xxhash 0.8.0 h35c211d_3 conda-forge xxmotif 1.6 0 bioconda xz 5.2.5 haf1e3a3_1 conda-forge yaml 0.2.5 haf1e3a3_0 conda-forge zlib 1.2.11 h7795811_1010 conda-forge zstd 1.5.0 h582d3a0_0 conda-forge
And finally, my input TXT file is this tab delimited file like this;
loc Trametinib_12h Trametinib_24h Trametinib_3h Untreated chr14:51533916-51534416 -0.73038978554192 -0.75756174613418 0.0292045064051196 1.45874702527098 chr17:40519037-40519537 -0.414261532842008 -0.791426003462628 -0.137144588165848 1.34283212447048 chr7:142808500-142809000 -0.856711011099945 -2.48554062398944 1.15561859563714 2.18663303945224 chr12:25458510-25459010 -1.11450907682427 -2.09368630465281 0.716401716886725 2.49179366459037 chr3:186098124-186098624 -0.813729589200967 -1.83892747430712 -1.08594276476826 3.73859982827634 chr20:62739893-62740393 -0.430940180607117 -0.893090704706988 -0.406246362173098 1.7302772474872 chr4:87896621-87897121 -0.577905813389179 0.05970737077861 -2.31475686197784 2.83295530458841 chr22:24207010-24207510 -0.603639756229142 -0.279537387442472 -0.948471767354042 1.83164891102566 chr11:122643118-122643618 -0.524114013826575 -0.749542504928305 -0.160310105579936 1.43396662433481 chr10:99965421-99965921 -1.06461687455462 -0.423861486523813 -0.450305165527713 1.93878352660615 chr11:70016462-70016962 -0.659396598158438 -1.30147785188861 -0.126278345089177 2.08715279513622 chr22:43264253-43264753 -0.858073997387409 -1.07580442926487 0.53618053094244 1.39769789570984 chr14:74616749-74617249 -0.540435607173403 -0.439786003323952 -0.210392283547632 1.19061389404499 chr9:19998659-19999159 -0.992356201003537 -1.68042041234842 0.598847799536313 2.07392881381564
With peak coordinates in the first column and normalised/mean centred values in the others for each group. I would really appreciate any help as I already tried in different ways but couldn't fix the problem Many thanks! Francesco