meme_4.11.4: make test failing on meme-chip

Jorge Boucas

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May 8, 2017, 9:37:29 AM5/8/17

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make test failing on meme-chip:

here the meme-chip.log

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Test meme-chip1 ...

meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.s &> log

Starting getsize: getsize results/meme-chip1/Klf1.100.s 1> $metrics

getsize ran successfully in 0.022734 seconds

Starting fasta-most: fasta-most -min 50 < results/meme-chip1/Klf1.100.s 1> $metrics

fasta-most ran successfully in 0.06341 seconds

Starting fasta-center: fasta-center -dna -len 100 < results/meme-chip1/Klf1.100.s 1> results/meme-chip1/seqs-centered

fasta-center ran successfully in 0.087317 seconds

Starting fasta-shuffle-letters: fasta-shuffle-letters results/meme-chip1/seqs-centered results/meme-chip1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1

fasta-shuffle-letters ran successfully in 0.0278 seconds

Starting fasta-get-markov: fasta-get-markov -nostatus -nosummary -dna -m 1 results/meme-chip1/Klf1.100.s results/meme-chip1/background

fasta-get-markov ran successfully in 0.027993 seconds

Starting meme: meme results/meme-chip1/seqs-centered -oc results/meme-chip1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile results/meme-chip1/background -dna -revcomp -nostatus

meme ran successfully in 27.290592 seconds

Starting dreme: dreme -v 1 -oc results/meme-chip1/dreme_out -png -dna -p results/meme-chip1/seqs-centered -n results/meme-chip1/seqs-shuffled

dreme ran successfully in 2.216163 seconds

Starting centrimo: centrimo -seqlen 500 -verbosity 1 -oc results/meme-chip1/centrimo_out -bfile results/meme-chip1/background results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.m

eme

centrimo ran successfully in 0.70559 seconds

Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile results/meme-chip1/background results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

tomtom ran successfully in 1.293705 seconds

Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile results/meme-chip1/background results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

tomtom ran successfully in 0.332577 seconds

Starting tomtom: tomtom -verbosity 1 -text -thresh 0.1 results/meme-chip1/combined.meme results/meme-chip1/combined.meme 1> results/meme-chip1/motif_alignment.txt

tomtom ran successfully in 0.221436 seconds

Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_1 -bgfile results/meme-chip1/background -primary WGGGYGTGGY results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.xml m

eme-chip/JASPAR_CORE_2014_vertebrates.meme

spamo ran successfully in 0.964339 seconds

Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_2 -bgfile results/meme-chip1/background -primary WGCYYCHBCCCTCYC results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.

xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

spamo ran successfully in 0.730784 seconds

Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_3 -bgfile results/meme-chip1/background -primary MA0140.2 results/meme-chip1/Klf1.100.s meme-chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.

xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

spamo ran successfully in 0.697921 seconds

Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-chip1/fimo_out_1 --bgfile results/meme-chip1/background --motif WGGGYGTGGY results/meme-chip1/meme_out/meme.xml results/meme-chip1/Klf1.100.s

fimo ran successfully in 0.084764 seconds

Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-chip1/fimo_out_2 --bgfile results/meme-chip1/background --motif WGCYYCHBCCCTCYC results/meme-chip1/meme_out/meme.xml results/meme-chip1/Klf1.100.s

fimo ran successfully in 0.078447 seconds

Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-chip1/fimo_out_3 --bgfile results/meme-chip1/background --motif MA0140.2 meme-chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/Klf1.100.s

fimo ran successfully in 0.143529 seconds

Starting meme-chip_html_to_tsv: meme-chip_html_to_tsv results/meme-chip1/meme-chip.html results/meme-chip1/summary.tsv

meme-chip_html_to_tsv exited with error code 2

-------------------------------------------------------------------------------

meme-chip did not create the file "results/meme-chip1/summary.tsv"

FAILED!

CharlesEGrant

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May 9, 2017, 4:44:31 PM5/9/17

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This error message usually indicates that you are missing one of the required Perl modules: HTML::TreeBuilder.pm. There should have been a warning message about this when you ran 'configure'. The section on prerequisite software in the installation guide may be helpful.

Devinder Kaur

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Aug 8, 2017, 9:11:32 AM8/8/17

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I was getting the same error but did not get resolved by installing Perl modules: HTML::TreeBuilder.pm
The same error appeared again.

Devinder Kaur

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Aug 8, 2017, 9:49:08 AM8/8/17

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I my testsuite (MEME Version 4.12.0) summary, from 108, 107 tests get passed except meme-chip1 (shown error of meme-chip: did not create the file "results/meme-chip1/summary.tsv").

I will use meme motif search and MAST only.
don't need MEME-Chip part. So, Can I proceed for make install with this one error?

Devinder Kaur

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Aug 8, 2017, 10:17:19 AM8/8/17

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Hi,

I sorted it out. All worked fine. Thanks to MEME google group and suggestions from you.

Jenny Shi

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Oct 25, 2017, 3:41:13 PM10/25/17

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Devinder,

I ran into the same issue. All missing perl modules have been added. Now I get

meme-chip did not create the file "results/meme-chip1/summary.tsv"

FAILED!

How did you resolve it?

Thanks,

Jenny

cegrant

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Nov 1, 2017, 4:27:58 PM11/1/17

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That message almost always means that either the JSON or HTML::Treebuilder Perl modules have not been installed. You can check if this is the problem by looking in the memechip_out directory, and checking the summary_msgs.txt file. The full error message describing the problem should be at the end of that file.

alexandre marand

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Feb 7, 2018, 10:12:09 AM2/7/18

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This solved the problem for me - cpanm JSON

i...@alum.mit.edu

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Feb 22, 2018, 3:06:10 PM2/22/18

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I would also like to know how you resolved it. I have installed all of the perl dependencies and am still getting this error. Thanks!

CharlesEGrant

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Feb 22, 2018, 8:17:20 PM2/22/18

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Which error? A couple of different errors have been discussed in this thread. Can you post the contents of tests/scripts/meme-chip.log?

Shaurya Jauhari

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Jul 9, 2018, 4:48:22 AM7/9/18

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I can second that. However, installing perl modules, viz. (i) XML::Simple (ii) HTML::Treebuilder, and (iii) JSON helped resolve this issue.

In addition, please care to glimpse through http://meme-suite.org/doc/install.html?man_type=web#prerequisite