Centrimo error: Template does not contain data section
3
2
Entering edit mode
2.8 years ago
Matus ▴ 50

Hello,

I am trying to run MEME-chip and I am experiencing problems with centrimo and spamo.

These two packages fail with Errror:

Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
FATAL: Template does not contain data section.

The centrimo was run as

centrimo --oc MEME/Test/centrimo_out --verbosity 1 --score 5.0 --ethresh 10.0 --bfile MEME/Test/Cluster_7.fa.bg MEME/Test/Cluster_7.fa /home/s1469622/dstore/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme /home/s1469622/dstore/motif_databases/MOUSE/uniprobe_mouse.meme

When I upload my fasta file on the web service everything works. The generated background file is identical to mine so I do not understand why it is failing.

Could you please help me with this?

Background file:

# 1-order Markov frequencies from file MEME/Test/Cluster_7.fa
# seqs: 1956    min: 500    max: 500    avg: 500.0    sum: 978000    alph: DNA
# order 0
A 2.487e-01
C 2.513e-01
G 2.513e-01
T 2.487e-01
# order 1
AA 7.168e-02
AC 5.016e-02
AG 7.936e-02
AT 4.752e-02
CA 7.227e-02
CC 7.526e-02
CG 2.443e-02
CT 7.936e-02
GA 6.274e-02
GC 6.313e-02
GG 7.526e-02
GT 5.016e-02
TA 4.200e-02
TC 6.274e-02
TG 7.227e-02
TT 7.168e-02

Example of Fasta

>chr1:3914040-3914540
ACTATTTTAAGTATCTGCTGTTTGGAATGGAGGCCACAGTCTGTATTTAACAGATTCTGCCACAGAATTTTTATAAGCCCAAGAAGAAGGAAAATTTCAATCTATATTGTTATATCCACTTTGATTTCTTTCAAATTATTCCAGCTCTAATCTTATGTGCAACAAGGAGCACAATGCCTTAACAGATGCAGAATGACATTCTTTGTCAACACAGGCTCTTTGCTTTTCTTTTGCAAATGCCAATGTCCAGCAGATAATTGTCATTTAGAAAGTGATGTATTATGAAGTTAATCAACCTTTTATAATTGAGGTTTTCCTTTCCTCTGTTTGCCGGATGAATTCAGTACCCCAGAATTTCTCATCACAGAAGGAACaaaaaaaaaaaaaaaaaaaaaaCCAACAACCAAAAAAATAATCATCTTTTCCCCTAATCTTAAGTTTATACACAATACCCTTTCACTTAGTAATTCAAGGTGGCTTCATTAGTCCAACATGTCCAG
>chr1:4857339-4857839
TGTCATTTTTTTACCGTGGCTTTTTTTAAGTCACAATTCTCAAGGCCGTCGTCTTTTTAGTCGGTTTTCATCAGCAGGCTAGATGGTTTGAATATCTGAGTCCAAGAGTGAGCCTCAGTGCTCATGCGCTTTAAGCCCTCGGCAATGCCTGTCCTGCGTCCCAGAGAACGCTCTGCCGGAGGGGTTTCGATGGAACTCGTAGCAACCTACCGCCTACTGCCTGATCCCTCTGGCGTGAAAGCCGGACTCCGTCCAACTCCAGCTCGCCAGCAACGCGAGTCCGGATAGGGCCGGAAGTTCCAGACTGCTGGGGGCGGGAATAGATTAAAAGAACAGCGCACGCCTGAGCGAGCCACTTCTACTTTCCAGTCTCCTGCGATCGATTCGTAGTGCCTGTGTGGCGCGCGCGGTGCTTGACTGGCACGGCCTAGGGGGCGGAGCGCTTATCCCTGCCGCCGCGGGCCGGGTCTGTGAGGAAGGCCTAGGCCAGCGGCTTCGCG
>chr1:4972323-4972823
caaaaGGGAGGCAGAGGGAGACAGAGACTGAGAAAGACAGACTGTTAGTTATCTTCAGCTTCTCCACTTCTAACTCAGCAAAACCAAATGAGCTTTCTATATCCCAGAAGCCTTTTGACTTTATCTTGACCTTGGGCCTAGATTTTGATGGAAATTTCTCTGTAATCCTGTTTCTGTTCTTCCTTTGAATAACTAAAGAAATGTAAAACTGTTGACCTTTTAGAGCATTGTACTCAGTCTTTCTCCCTCTGAAGCAGTGGAAATAAGACTTAGGTAGAAAGGTTATTGATTTCCGGTCAAGTGTGTACTGACTGCAAAGCCCCTTTCATTGTGGGCAGCTAAGAAGGTAAATGCGgttcctctttctccacatccttgccagcatctgctgtcacctgaacttttgatcttagccattctgactgctgtgaggtggaatctcagagttgttttgatttgcatttccctgatgtttaaggatgttgaacattttttcaggt
>chr1:7052296-7052796
ATGGATTGCCTTGCTTttctttctttctggacaggtcctcaagtggtattccaggccagtcacggactcataatgtattttaggctggcctgcagtttacagcctcagcttctacagtgctagctggtgttagatttcaacccccacccccccaacaaatgcacaatgtacctatttaacatattcaagccgactaagatctccctgcatcctgcaggccctacctgctaccctacttgctacagggttgtcataccctgcccccaccctgagttctccatctctaggggatgagctgcccttcccttagctactcttctctGAtgttgattttcaaagctgagacaactggccgaggtgcctatttatcatatcaagctgaccaggttaccaggttctcccaacgtccctcagtcactttctacttgttacaaggtgtggctagcattttataccctctaccctgagctctgtcactggggctttgctgctcttctgcc
>chr1:7297803-7298303
ctgtgttttttcacaaaaagaagacagagcatgatggctgcctgagagattagttcgtcaactggacacagatcctgaatcttctagtaagtatgactctaaccttgattatggttaaaaaccctctttagctgaaaagttaatttggagcacagcctccactcccagagcagcctttctgcaattctcaaagtcacctccctcacatcgggagctctaagtctaagccgcctgatcgttgctcatttgcaactgaagggattacctggactttcccaaagaagcttttgtactgttgcttttcactgtcttgactttgtttttcaagcaggtcagtcaatgcccttcagcctgactgcagcaagcatgcatccctgcctccaacagtgcagatggcgttattaatcttcattcaagaagcattctaagtatatattgtggcttttggtctgatttgggaataaggtttgctatgagagccagacagtctaagataggca
ChIP-Seq MEME • 3.3k views
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0
Entering edit mode

Hi, not sure if this might help you. A quick-and-dirty version of your command yields an output without problems for me, albeit with no enriched motifs for the sample sequences you provided. Here is what I tried: centrimo --oc centrimo_out --verbosity 1 --score 5.0 --ethresh 10.0 --bfile Cluster_7.fa.bg Cluster_7.fa uniprobe_mouse.meme

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0
Entering edit mode

Hello Anima,

Thank you for your reply. I think the problem is in the motif database because the minimal example I provided gives me an error and the only difference is the meme database.

Could you give me an example how it should look like? I downloaded mine from: http://meme-suite.org/doc/download.html The top 50 lines of JASPAR2018_CORE_vertebrates_non-redundant.meme

MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies A 0.25 C 0.25 G 0.25 T 0.25

MOTIF MA0004.1 Arnt letter-probability matrix: alength= 4 w= 6 nsites= 20 E= 0
 0.200000  0.800000  0.000000  0.000000
 0.950000  0.000000  0.050000  0.000000
 0.000000  1.000000  0.000000  0.000000
 0.000000  0.000000  1.000000  0.000000
 0.000000  0.000000  0.000000  1.000000
 0.000000  0.000000  1.000000  0.000000 URL http://jaspar2018.genereg.net/matrix/MA0004.1

MOTIF MA0006.1 Ahr::Arnt letter-probability matrix: alength= 4 w= 6 nsites= 24 E= 0
 0.125000  0.333333  0.083333  0.458333
 0.000000  0.000000  0.958333  0.041667
 0.000000  0.958333  0.000000  0.041667
 0.000000  0.000000  0.958333  0.041667
 0.000000  0.000000  0.000000  1.000000
 0.000000  0.000000  1.000000  0.000000 URL http://jaspar2018.genereg.net/matrix/MA0006.1

MOTIF MA0019.1 Ddit3::Cebpa letter-probability matrix: alength= 4 w= 12 nsites= 39 E= 0
 0.358974  0.179487  0.307692  0.153846
 0.282051  0.179487  0.358974  0.179487
 0.461538  0.076923  0.384615  0.076923
 0.000000  0.025641  0.000000  0.974359
 0.000000  0.000000  0.974359  0.025641
 0.102564  0.846154  0.000000  0.051282
 0.974359  0.025641  0.000000  0.000000
 0.923077  0.051282  0.025641  0.000000
 0.000000  0.153846  0.000000  0.846154
 0.358974  0.435897  0.128205  0.076923
 0.102564  0.589744  0.230769  0.076923
 0.000000  0.666667  0.153846  0.179487 URL http://jaspar2018.genereg.net/matrix/MA0019.1

MOTIF MA0025.1 NFIL3 letter-probability matrix: alength= 4 w= 11 nsites= 23 E= 0
 0.043478  0.000000  0.000000  0.956522
 0.000000  0.000000  0.086957  0.913043
 0.956522  0.000000  0.000000  0.043478
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3
Entering edit mode
2.7 years ago
Matus ▴ 50

Hello,

I emailed developers of meme-suite and they pointed that the error comes from centrimo or spamo being able to access template html file. This suggests that the conda installation of meme did not worked properly.

I have solved the problem by installing meme-suite using

conda install -c bioconda/label/cf201901 meme

instead of

conda install -c bioconda meme

Matus

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2
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Thanks for this. conda install 'meme=5.0.2' 'icu=58.2' may be more explicit than conda install bioconda/label/cf201901 meme

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1
Entering edit mode

it works. Thanks! I tested, ame and centrimo commands failed in meme 5.0.5 in conda version.

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0
Entering edit mode

Problem solved then, good job ;)

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0
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Hello, I am having exactly the same error when trying to run AME with motif files (in .meme format) downloaded either from JASPAR or MEME. Using the alternative conda install (conda install -c bioconda/label/cf201901 meme) did not help. Has anyone had the same issue and solved it?

Update after 40 minutes ... conda install -c bioconda/label/cf201901 meme did not work, but conda install 'meme=5.0.2' 'icu=58.2' worked (thanks! dariober). It looks like an older version of meme (that requires a conda environment with python 2.7) but at least it runs...

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0
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Dear Matus and Dario. Thank you for the explanation.

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1
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18 months ago

If any useful, this is how I installed the latest meme (5.3.0) using a mixture of conda and source code

  • Create a conda environment with these dependencies:

    - python >=3.0
    - perl =5.22.0.1
    - zlib
    - ghostscript
    - perl-xml-parser
    - perl-yaml
    - perl-xml-simple
    - perl-html-template
    - perl-cgi
    - perl-html-parser
    - perl-html-tree
    - perl-math-cdf
    - perl-log-log4perl
    - perl-json
    - perl-file-which
    

I think the perl version perl =5.22.0.1 is important because of this (bio)conda issue

  • In the new conda envirnoment, download, compile and install meme:

    DIR=/full/path/to/your/installation/dir
    
    rm -f meme-5.3.0.tar.gz
    rm -rf meme-5.3.0
    
    wget http://meme-suite.org/meme-software/5.3.0/meme-5.3.0.tar.gz
    tar zxvf meme-5.3.0.tar.gz
    rm meme-5.3.0.tar.gz
    cd meme-5.3.0
    
    ./configure --prefix=$DIR --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt
    make clean
    make &> make.log
    make test &> test.log || true
    make install &> install.log
    
    export PATH=$DIR/bin:$DIR/libexec/meme-5.3.0:$PATH
    meme-chip -version
    tomtom -version
    
  • Before using meme, execute

    export PATH=$DIR/bin:$DIR/libexec/meme-5.3.0:$PATH
    

or add those paths to your profile.

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0
Entering edit mode
2.8 years ago
Anima Mundi ★ 2.9k

Hi again, I see what is causing the error.

It looks like your database JASPAR2018_CORE_vertebrates_non-redundant.meme needs some reformatting. For each motif you provided, I just truncated header line, setting letter-probability... as a second line, i.e.:

MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies
A 0.25 C 0.25 G 0.25 T 0.25

MOTIF MA0004.1 Arnt
letter-probability matrix: alength= 4 w= 6 nsites= 20 E= 0
 0.200000  0.800000  0.000000  0.000000
 0.950000  0.000000  0.050000  0.000000
 0.000000  1.000000  0.000000  0.000000
 0.000000  0.000000  1.000000  0.000000
 0.000000  0.000000  0.000000  1.000000
 0.000000  0.000000  1.000000  0.000000
 URL http://jaspar2018.genereg.net/matrix/MA0004.1

MOTIF MA0006.1 Ahr::Arnt
letter-probability matrix: alength= 4 w= 6 nsites= 24 E= 0
 0.125000  0.333333  0.083333  0.458333
 0.000000  0.000000  0.958333  0.041667
 0.000000  0.958333  0.000000  0.041667
 0.000000  0.000000  0.958333  0.041667
 0.000000  0.000000  0.000000  1.000000
 0.000000  0.000000  1.000000  0.000000
 URL http://jaspar2018.genereg.net/matrix/MA0006.1

MOTIF MA0019.1 Ddit3::Cebpa
letter-probability matrix: alength= 4 w= 12 nsites= 39 E= 0
 0.358974  0.179487  0.307692  0.153846
 0.282051  0.179487  0.358974  0.179487
 0.461538  0.076923  0.384615  0.076923
 0.000000  0.025641  0.000000  0.974359
 0.000000  0.000000  0.974359  0.025641
 0.102564  0.846154  0.000000  0.051282
 0.974359  0.025641  0.000000  0.000000
 0.923077  0.051282  0.025641  0.000000
 0.000000  0.153846  0.000000  0.846154
 0.358974  0.435897  0.128205  0.076923
 0.102564  0.589744  0.230769  0.076923
 0.000000  0.666667  0.153846  0.179487
 URL http://jaspar2018.genereg.net/matrix/MA0019.1

I also set URLs as separate lines, though this does not seem to be required. After these changes, I could get results with:

centrimo --oc centrimo_out --verbosity 1 --score 5.0 --ethresh 10.0 --bfile Cluster_7.fa.bg Cluster_7.fa uniprobe_mouse.meme JASPAR2018_CORE_vertebrates_non-redundant.meme

By the way, some months ago I retrieved Jaspar Core (2018) matrices from here (downloaded as a folder containing single PSWMs, condensed in a file using (from that folder): for e in *.meme; do cat $e >> JASPAR2018_CORE_vertebrates_non-redundant_pfms_meme.meme; done).

Hope this helps!

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0
Entering edit mode

Hello Anima,

Thank you very much for your help.

Unfortunately, formatting The database didn't help.

I even reinstall my conda but it didn't help either I am really clueless at this point.

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0
Entering edit mode

Mmm, I see. Using the Jaspar database I suggested on your minimal example fixes the problem? And using uniprobe_mouse.meme only?

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