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snystrom / memes

An R interface to the MEME Suite
https://snystrom.github.io/memes/
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path problems #105

Open theokirkland opened 1 year ago

theokirkland commented 1 year ago

I installed meme with macports on a mac

The program is in /opt/local/share/meme-5.5.0.

I used this in R options(meme_bin = "/opt/local/share/meme-5.5.0")

when I check_meme_install

there is a green check mark beside checking main install but all the other have red xs.

What am I doing wrong?

snystrom commented 1 year ago

Can you post the output from the terminal of ls /opt/local/share/meme-5.5.0/*? Alternately, from inside R: list.files("/opt/local/share/meme-5.5.0/", recursive = TRUE)?

I wonder if the macports version has a different file structure than expected. Or if it only installed meme but not the other tools. Can you call ame or tomtom, etc. from the commandline?

snystrom commented 1 year ago

Oh also just for completeness, could you post the full check_meme_install() output as well as the output of sessionInfo()?

theokirkland commented 1 year ago

Thanks for your quick response. The files you requested are attached. However, I figured out how to make things work by using

options(meme_bin = "/opt/local/bin”)

However, I’m having trouble understanding your tutorial. Once I downloaded the BSgenome.Dmelanogaster.UCSC.dm6 from Bioconductor the code worked fine but the output kept saying

[Note: incomplete universalmotif_df object.]

Am I not understanding something?

My goal is to look for motifs in a set of fasta files and compare to a control set of fasta files looking for enrichment. I have loaded the sequences from gtf files into GenomicFeatures, found overlaps of interest and exported the data as bed files. Then used getfasta from bedrolls to get fasta files. Up until now I’ve used an old program named clover to get enrichment, but I would like to compare the results to meme. Do you have any suggestions about this?

Thanks for all your help,

Theo



On Feb 17, 2023, at 4:46 AM, Spencer Nystrom @.***> wrote:

list.files("/opt/local/share/meme-5.5.0/", recursive = TRUE)

$ ls /opt/local/share/meme-5.5.0/* /opt/local/share/meme-5.5.0/Docker.Readme.md /opt/local/share/meme-5.5.0/RSATWS.fungi.wsdl /opt/local/share/meme-5.5.0/RSATWS.metazoa.wsdl /opt/local/share/meme-5.5.0/RSATWS.plants.wsdl /opt/local/share/meme-5.5.0/RSATWS.prokaryotes.wsdl /opt/local/share/meme-5.5.0/RSATWS.protists.wsdl /opt/local/share/meme-5.5.0/alphabet_utilities.js /opt/local/share/meme-5.5.0/ame_doc.js /opt/local/share/meme-5.5.0/ame_icon.png /opt/local/share/meme-5.5.0/ame_template.css /opt/local/share/meme-5.5.0/ame_template.html /opt/local/share/meme-5.5.0/ame_template.js /opt/local/share/meme-5.5.0/beadstring.xsl /opt/local/share/meme-5.5.0/block_diagram.css /opt/local/share/meme-5.5.0/block_diagram.js /opt/local/share/meme-5.5.0/centrimo_doc.js /opt/local/share/meme-5.5.0/centrimo_graph.js /opt/local/share/meme-5.5.0/centrimo_icon.png /opt/local/share/meme-5.5.0/centrimo_template.css /opt/local/share/meme-5.5.0/centrimo_template.html /opt/local/share/meme-5.5.0/centrimo_template.js /opt/local/share/meme-5.5.0/cisml-to-gff.xsl /opt/local/share/meme-5.5.0/cisml-to-gff3.xsl /opt/local/share/meme-5.5.0/cisml-to-html.xsl /opt/local/share/meme-5.5.0/cisml-to-text.xsl /opt/local/share/meme-5.5.0/cisml.css /opt/local/share/meme-5.5.0/citation.js /opt/local/share/meme-5.5.0/citation.js.h /opt/local/share/meme-5.5.0/citation.js.pm /opt/local/share/meme-5.5.0/citation.js.xsl /opt/local/share/meme-5.5.0/constants.js /opt/local/share/meme-5.5.0/constants.js.xsl /opt/local/share/meme-5.5.0/constants.xsl /opt/local/share/meme-5.5.0/db_general.csv /opt/local/share/meme-5.5.0/db_other_genomes.csv /opt/local/share/meme-5.5.0/delay_draw.js /opt/local/share/meme-5.5.0/description_section.js /opt/local/share/meme-5.5.0/discovery_doc.js /opt/local/share/meme-5.5.0/dreme_icon.png /opt/local/share/meme-5.5.0/dreme_template.css /opt/local/share/meme-5.5.0/dreme_template.html /opt/local/share/meme-5.5.0/dreme_template.js /opt/local/share/meme-5.5.0/eps_context.js /opt/local/share/meme-5.5.0/fimo_doc.js /opt/local/share/meme-5.5.0/generate_js_wrapped_template.pl /opt/local/share/meme-5.5.0/generate_xsl_icons.pl /opt/local/share/meme-5.5.0/gomo-to-html.xsl /opt/local/share/meme-5.5.0/gomo_doc.js /opt/local/share/meme-5.5.0/gomo_doc.js.xsl /opt/local/share/meme-5.5.0/hmm-text.xsl /opt/local/share/meme-5.5.0/icons.xsl /opt/local/share/meme-5.5.0/job_status.tmpl /opt/local/share/meme-5.5.0/logging.conf /opt/local/share/meme-5.5.0/mast_icon.png /opt/local/share/meme-5.5.0/mast_template.css /opt/local/share/meme-5.5.0/mast_template.html /opt/local/share/meme-5.5.0/mast_template.js /opt/local/share/meme-5.5.0/mcast_doc.js /opt/local/share/meme-5.5.0/mcast_icon.png /opt/local/share/meme-5.5.0/mcast_template.css /opt/local/share/meme-5.5.0/mcast_template.html /opt/local/share/meme-5.5.0/mcast_template.js /opt/local/share/meme-5.5.0/meme-chip_doc.js /opt/local/share/meme-5.5.0/meme-chip_template.css /opt/local/share/meme-5.5.0/meme-chip_template.html /opt/local/share/meme-5.5.0/meme-chip_template.js /opt/local/share/meme-5.5.0/meme.css /opt/local/share/meme-5.5.0/meme.css.xsl /opt/local/share/meme-5.5.0/meme_icon.png /opt/local/share/meme-5.5.0/meme_template.css /opt/local/share/meme-5.5.0/meme_template.html /opt/local/share/meme-5.5.0/meme_template.js /opt/local/share/meme-5.5.0/memechip_icon.png /opt/local/share/meme-5.5.0/momo_doc.js /opt/local/share/meme-5.5.0/momo_icon.png /opt/local/share/meme-5.5.0/momo_template.css /opt/local/share/meme-5.5.0/momo_template.html /opt/local/share/meme-5.5.0/momo_template.js /opt/local/share/meme-5.5.0/motif_logo.js /opt/local/share/meme-5.5.0/motif_logo_template.js /opt/local/share/meme-5.5.0/new_icon.png /opt/local/share/meme-5.5.0/prior1.plib /opt/local/share/meme-5.5.0/prior30.plib /opt/local/share/meme-5.5.0/sea_doc.js /opt/local/share/meme-5.5.0/sea_icon.png /opt/local/share/meme-5.5.0/sea_template.css /opt/local/share/meme-5.5.0/sea_template.html /opt/local/share/meme-5.5.0/sea_template.js /opt/local/share/meme-5.5.0/set_maxtime.pl /opt/local/share/meme-5.5.0/simple-shared-doc.js /opt/local/share/meme-5.5.0/simple-shared-doc.js.xsl /opt/local/share/meme-5.5.0/site_histogram.js /opt/local/share/meme-5.5.0/spamo_doc.js /opt/local/share/meme-5.5.0/spamo_graph.js /opt/local/share/meme-5.5.0/spamo_icon.png /opt/local/share/meme-5.5.0/spamo_template.css /opt/local/share/meme-5.5.0/spamo_template.html /opt/local/share/meme-5.5.0/spamo_template.js /opt/local/share/meme-5.5.0/streme_doc.js /opt/local/share/meme-5.5.0/streme_icon.png /opt/local/share/meme-5.5.0/streme_template.css /opt/local/share/meme-5.5.0/streme_template.html /opt/local/share/meme-5.5.0/streme_template.js /opt/local/share/meme-5.5.0/submit_or_download_motif.js /opt/local/share/meme-5.5.0/template.eps /opt/local/share/meme-5.5.0/template.js /opt/local/share/meme-5.5.0/tgene_doc.js /opt/local/share/meme-5.5.0/tgene_icon.png /opt/local/share/meme-5.5.0/tgene_template.css /opt/local/share/meme-5.5.0/tgene_template.html /opt/local/share/meme-5.5.0/tgene_template.js /opt/local/share/meme-5.5.0/tomtom_doc.js /opt/local/share/meme-5.5.0/tomtom_icon.png /opt/local/share/meme-5.5.0/tomtom_template.css /opt/local/share/meme-5.5.0/tomtom_template.html /opt/local/share/meme-5.5.0/tomtom_template.js /opt/local/share/meme-5.5.0/utilities.js /opt/local/share/meme-5.5.0/utilities.js.xsl /opt/local/share/meme-5.5.0/xstreme_doc.js /opt/local/share/meme-5.5.0/xstreme_icon.png /opt/local/share/meme-5.5.0/xstreme_template.css /opt/local/share/meme-5.5.0/xstreme_template.html /opt/local/share/meme-5.5.0/xstreme_template.js

/opt/local/share/meme-5.5.0/doc: GLAM2_method.pdf fasta-shuffle-letters.html momo-output-format.html alphabet-format.html fasta-subsample.html momo.html alphabets.html fasta-unique-names.html motif-consensus.html alphtype.html fimo-output-format.html motif-shuffle-columns.html ama-qvalues.html fimo-tutorial.html motif_conversion.html ama.html fimo.html motiph.html ame-output-format.html fisher_exact.html news.txt ame-tutorial.html fitevd.html nmica2meme.html ame.html gendb.html overview.html authors.html general-faq.html pmp_bf.html beadstring.html getsize.html prior30.plib bed-format.html glam2.html priority2meme.html bed2fasta.html glam2_alphabet.html prosite2meme.html beeml2meme.html glam2_tut.html psm-format.html bfile-format.html glam2format.html psp-format.html centrimo-output-format.html glam2mask.html psp-gen.html centrimo-tutorial.html glam2scan.html purge.html centrimo.html godag-format.html qvalue.html ceqlogo.html gomo-output-format.html reconcile-tree-alignment.html chen2meme.html gomo.html reduce-alignment.html cite.html gomo_highlight.html release-notes.html clustalw-format.html images remove-alignment-gaps.html clustalw2fasta.html install.html rna2meme.html clustalw2phylip.html ismb94.pdf scpd2meme.html compute-prior-dist.html iupac.html scripting.html compute-uniform-priors.html iupac2meme.html sea-output-format.html copyright.html jaspar2meme.html sea.html create-priors.html js server_down.html css log-hmm.html shadow.html dmix-format.html mast.html sites2meme.html download-index.html matrix2meme.html spamo-output-format.html download.html mcast-output-format.html spamo.html draw-mhmm.html mcast.html streme-output-format.html dreme-tutorial.html meme-chip-output-format.html streme-tutorial.html dreme.html meme-chip.html streme.html dust.html meme-format.html taipale2meme.html elm2meme.html meme-get-motif.html tamo2meme.html examples meme-rename.html tgene-output-format.html fasta-center.html meme.html tgene-tutorial.html fasta-dinucleotide-shuffle.html meme2alph.html tgene.html fasta-fetch.html meme2images.html tomtom-output-format.html fasta-format.html meme2meme.html tomtom.html fasta-get-markov.html mhmm-format.html transfac-format.html fasta-grep.html mhmm.html transfac2meme.html fasta-hamming-enrich.html mhmm2html.html uniprobe2meme.html fasta-holdout-set.html mhmme.html update-sequence-db.html fasta-io.html mhmms.html xstreme-output-format.html fasta-make-index.html mhmmscan-format.html xstreme.html fasta-most.html mhmmscan.html

within R

list.files("/opt/local/share/meme-5.5.0/", recursive = TRUE)

"alphabet_utilities.js"
[2] "ame_doc.js"
[3] "ame_icon.png"
[4] "ame_template.css"
[5] "ame_template.html"
[6] "ame_template.js"
[7] "beadstring.xsl"
[8] "block_diagram.css"
[9] "block_diagram.js"
[10] "centrimo_doc.js"
[11] "centrimo_graph.js"
[12] "centrimo_icon.png"
[13] "centrimo_template.css"
[14] "centrimo_template.html"
[15] "centrimo_template.js"
[16] "cisml-to-gff.xsl"
[17] "cisml-to-gff3.xsl"
[18] "cisml-to-html.xsl"
[19] "cisml-to-text.xsl"
[20] "cisml.css"
[21] "citation.js"
[22] "citation.js.h"
[23] "citation.js.pm"
[24] "citation.js.xsl"
[25] "constants.js"
[26] "constants.js.xsl"
[27] "constants.xsl"
[28] "db_general.csv"
[29] "db_other_genomes.csv"
[30] "delay_draw.js"
[31] "description_section.js"
[32] "discovery_doc.js"
[33] "doc/alphabet-format.html"
[34] "doc/alphabets.html"
[35] "doc/alphtype.html"
[36] "doc/ama-qvalues.html"
[37] "doc/ama.html"
[38] "doc/ame-output-format.html"
[39] "doc/ame-tutorial.html"
[40] "doc/ame.html"
[41] "doc/authors.html"
[42] "doc/beadstring.html"
[43] "doc/bed-format.html"
[44] "doc/bed2fasta.html"
[45] "doc/beeml2meme.html"
[46] "doc/bfile-format.html"
[47] "doc/centrimo-output-format.html"
[48] "doc/centrimo-tutorial.html"
[49] "doc/centrimo.html"
[50] "doc/ceqlogo.html"
[51] "doc/chen2meme.html"
[52] "doc/cite.html"
[53] "doc/clustalw-format.html"
[54] "doc/clustalw2fasta.html"
[55] "doc/clustalw2phylip.html"
[56] "doc/compute-prior-dist.html"
[57] "doc/compute-uniform-priors.html"
[58] "doc/copyright.html"
[59] "doc/create-priors.html"
[60] "doc/css/menu.css"
[61] "doc/css/style.css"
[62] "doc/dmix-format.html"
[63] "doc/download-index.html"
[64] "doc/download.html"
[65] "doc/draw-mhmm.html"
[66] "doc/dreme-tutorial.html"
[67] "doc/dreme.html"
[68] "doc/dust.html"
[69] "doc/elm2meme.html"
[70] "doc/examples/ame_example_output_files/ame.html"
[71] "doc/examples/ame_example_output_files/ame.tsv"
[72] "doc/examples/ame_example_output_files/sequences.tsv"
[73] "doc/examples/bed2fasta_example_output_files/Rxra.fa"
[74] "doc/examples/centrimo_example_output_files/centrimo.html"
[75] "doc/examples/centrimo_example_output_files/centrimo.tsv"
[76] "doc/examples/centrimo_example_output_files/site_counts.txt"
[77] "doc/examples/compute_prior_dist_example_output_files/prior.dist.txt"
[78] "doc/examples/create_examples.pl.in"
[79] "doc/examples/dreme_example_output_files/dreme.html"
[80] "doc/examples/dreme_example_output_files/dreme.txt"
[81] "doc/examples/dreme_example_output_files/dreme.xml"
[82] "doc/examples/dreme_example_output_files/m01nc_CCMCRCCC.png"
[83] "doc/examples/dreme_example_output_files/m01rc_GGGYGKGG.png"
[84] "doc/examples/dreme_example_output_files/m02nc_BTTATCW.png"
[85] "doc/examples/dreme_example_output_files/m02rc_WGATAAV.png"
[86] "doc/examples/dreme_example_output_files/m03nc_MCRCCCA.png"
[87] "doc/examples/dreme_example_output_files/m03rc_TGGGYGK.png"
[88] "doc/examples/dreme_example_output_files/m04nc_RARGAAA.png"
[89] "doc/examples/dreme_example_output_files/m04rc_TTTCYTY.png"
[90] "doc/examples/dreme_example_output_files/m05nc_AKAAAM.png"
[91] "doc/examples/dreme_example_output_files/m05rc_KTTTMT.png"
[92] "doc/examples/dreme_example_output_files/m06nc_CTGTSTS.png"
[93] "doc/examples/dreme_example_output_files/m06rc_SASACAG.png"
[94] "doc/examples/dreme_example_output_files/m07nc_AGGGCGK.png"
[95] "doc/examples/dreme_example_output_files/m07rc_MCGCCCT.png"
[96] "doc/examples/dreme_example_output_files/m08nc_CCTKCCY.png"
[97] "doc/examples/dreme_example_output_files/m08rc_RGGMAGG.png"
[98] "doc/examples/dreme_example_output_files/m09nc_TTAAAAW.png"
[99] "doc/examples/dreme_example_output_files/m09rc_WTTTTAA.png"
[100] "doc/examples/dreme_example_output_files/m10nc_AAATAH.png"
[101] "doc/examples/dreme_example_output_files/m10rc_DTATTT.png"
[102] "doc/examples/dreme_example_output_files/m11nc_CATYTCC.png"
[103] "doc/examples/dreme_example_output_files/m11rc_GGARATG.png"
[104] "doc/examples/dreme_example_output_files/m12nc_CAGMCAC.png"
[105] "doc/examples/dreme_example_output_files/m12rc_GTGKCTG.png"
[106] "doc/examples/dreme_example_output_files/m13nc_CACAGY.png"
[107] "doc/examples/dreme_example_output_files/m13rc_RCTGTG.png"
[108] "doc/examples/dreme_example_output_files/m14nc_CTGGRGA.png"
[109] "doc/examples/dreme_example_output_files/m14rc_TCYCCAG.png"
[110] "doc/examples/dreme_example_output_files/m15nc_SACGTGA.png"
[111] "doc/examples/dreme_example_output_files/m15rc_TCACGTS.png"
[112] "doc/examples/example-datasets.mk"
[113] "doc/examples/example-datasets/adh.faa"
[114] "doc/examples/example-datasets/adh.meme"
[115] "doc/examples/example-datasets/At.faa"
[116] "doc/examples/example-datasets/At.glam2"
[117] "doc/examples/example-datasets/crp0.fna"
[118] "doc/examples/example-datasets/crp0.meme"
[119] "doc/examples/example-datasets/dpinteract_subset.meme"
[120] "doc/examples/example-datasets/dpinteract.meme"
[121] "doc/examples/example-datasets/Klf1.fna"
[122] "doc/examples/example-datasets/Klf1.meme"
[123] "doc/examples/example-datasets/lex0.fna"
[124] "doc/examples/example-datasets/mm9_tss_500bp_sampled_1000.fna"
[125] "doc/examples/example-datasets/nrmix.nseqs.100.100bp.seed.1.fa"
[126] "doc/examples/example-datasets/P300.chr21.bed"
[127] "doc/examples/example-datasets/Rxra.bed"
[128] "doc/examples/example-datasets/some_vertebrates.meme"
[129] "doc/examples/example-datasets/STRGGTCAN.meme"
[130] "doc/examples/examples.mk"
[131] "doc/examples/fimo_example_output_files/cisml.xml"
[132] "doc/examples/fimo_example_output_files/fimo.gff"
[133] "doc/examples/fimo_example_output_files/fimo.html"
[134] "doc/examples/fimo_example_output_files/fimo.tsv"
[135] "doc/examples/fimo_example_output_files/fimo.xml"
[136] "doc/examples/glam2_example_output_files/glam2.html"
[137] "doc/examples/glam2_example_output_files/glam2.meme"
[138] "doc/examples/glam2_example_output_files/glam2.txt"
[139] "doc/examples/glam2_example_output_files/logo_ssc1.eps"
[140] "doc/examples/glam2_example_output_files/logo_ssc1.png"
[141] "doc/examples/glam2_example_output_files/logo_ssc10.eps"
[142] "doc/examples/glam2_example_output_files/logo_ssc10.png"
[143] "doc/examples/glam2_example_output_files/logo_ssc2.eps"
[144] "doc/examples/glam2_example_output_files/logo_ssc2.png"
[145] "doc/examples/glam2_example_output_files/logo_ssc3.eps"
[146] "doc/examples/glam2_example_output_files/logo_ssc3.png"
[147] "doc/examples/glam2_example_output_files/logo_ssc4.eps"
[148] "doc/examples/glam2_example_output_files/logo_ssc4.png"
[149] "doc/examples/glam2_example_output_files/logo_ssc5.eps"
[150] "doc/examples/glam2_example_output_files/logo_ssc5.png"
[151] "doc/examples/glam2_example_output_files/logo_ssc6.eps"
[152] "doc/examples/glam2_example_output_files/logo_ssc6.png"
[153] "doc/examples/glam2_example_output_files/logo_ssc7.eps"
[154] "doc/examples/glam2_example_output_files/logo_ssc7.png"
[155] "doc/examples/glam2_example_output_files/logo_ssc8.eps"
[156] "doc/examples/glam2_example_output_files/logo_ssc8.png"
[157] "doc/examples/glam2_example_output_files/logo_ssc9.eps"
[158] "doc/examples/glam2_example_output_files/logo_ssc9.png"
[159] "doc/examples/glam2_example_output_files/logo1.eps"
[160] "doc/examples/glam2_example_output_files/logo1.png"
[161] "doc/examples/glam2_example_output_files/logo10.eps"
[162] "doc/examples/glam2_example_output_files/logo10.png"
[163] "doc/examples/glam2_example_output_files/logo2.eps"
[164] "doc/examples/glam2_example_output_files/logo2.png"
[165] "doc/examples/glam2_example_output_files/logo3.eps"
[166] "doc/examples/glam2_example_output_files/logo3.png"
[167] "doc/examples/glam2_example_output_files/logo4.eps"
[168] "doc/examples/glam2_example_output_files/logo4.png"
[169] "doc/examples/glam2_example_output_files/logo5.eps"
[170] "doc/examples/glam2_example_output_files/logo5.png"
[171] "doc/examples/glam2_example_output_files/logo6.eps"
[172] "doc/examples/glam2_example_output_files/logo6.png"
[173] "doc/examples/glam2_example_output_files/logo7.eps"
[174] "doc/examples/glam2_example_output_files/logo7.png"
[175] "doc/examples/glam2_example_output_files/logo8.eps"
[176] "doc/examples/glam2_example_output_files/logo8.png"
[177] "doc/examples/glam2_example_output_files/logo9.eps"
[178] "doc/examples/glam2_example_output_files/logo9.png"
[179] "doc/examples/glam2-aa-alph.txt"
[180] "doc/examples/glam2-dna-alph.txt"
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theokirkland commented 1 year ago

I have attached the file you requested.

After looking at the $PATH closely I entered

options(meme_bin = "/opt/local/bin") in R and it worked

However, I’m having trouble understanding your tutorial. Once I downloaded the BSgenome.Dmelanogaster.UCSC.dm6 from Bioconductor the code worked fine but the output kept saying

[Note: incomplete universalmotif_df object.]

Am I not understanding something?

My goal is to look for motifs in a set of fasta files and compare to a control set of fasta files looking for enrichment. I have loaded the sequences from gtf files into GenomicFeatures, found overlaps of interest and exported the data as bed files. Then used getfasta from bedrolls to get fasta files. Up until now I’ve used an old program named clover to get enrichment, but I would like to compare the results to meme. Do you have any suggestions about this?

Thanks for all your help,

Theo

snystrom commented 1 year ago

Hi Theo,

Glad you figured out the PATH issue. Could you please post the code you are running that produces that [Note: incomplete universalmotif_df object.] output error, and also post the sessionInfo() output?

I'll take a look this evening & try to write a more detailed answer to your process question as well once I get those.

Cheers.