Problem running MAST with motif file - error code 1

[margi...@gmail.com]

Hi all,

I'm having problems getting a motif file in the right format to run with MAST. This is my motif file (letter prob. frequencies were generated from PFMs from Wormbase):

My motif file:

MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies
A 0.339000 C 0.162000 G 0.162000 T 0.339000

MOTIF daf-16
letter-probability matrix: alength= 4 w= 14 nsites= 25

0.1739130 0.1304348 0.39130435 0.3043478
0.1666667 0.1250000 0.29166667 0.4166667
0.1600000 0.1600000 0.48000000 0.2000000
0.0400000 0.0000000 0.04000000 0.9200000
0.0000000 0.0000000 0.00000000 1.0000000
0.0400000 0.0000000 0.96000000 0.0000000
0.0000000 0.0000000 0.00000000 1.0000000
0.0000000 0.0400000 0.00000000 0.9600000
0.0000000 0.0000000 0.00000000 1.0000000
0.8800000 0.0000000 0.08000000 0.0400000
0.0000000 0.8400000 0.00000000 0.1600000
0.4166667 0.1250000 0.25000000 0.2083333
0.3478261 0.2173913 0.13043478 0.3043478
0.1363636 0.4545455 0.04545455 0.3636364

MOTIF skn-1
letter-probability matrix alength=4 w=12 nsites=33
0.18939394 0.37121212 0.09848485 0.3409091
0.51515152 0.12121212 0.06060606 0.3030303
0.42424242 0.06060606 0.09090909 0.4242424
0.21969697 0.09848485 0.03787879 0.6439394
0.42424242 0.00000000 0.57575758 0.0000000
0.00000000 0.00000000 0.00000000 1.0000000
0.00000000 1.00000000 0.00000000 0.0000000
1.00000000 0.00000000 0.00000000 0.0000000
0.00000000 0.00000000 0.00000000 1.0000000
0.03030303 0.45454545 0.27272727 0.2424242
0.39393939 0.36363636 0.06060606 0.1818182
0.36363636 0.21212121 0.06060606 0.3636364

MOTIF tra-1
letter-probability matrix alength=4 w=23 nsites=42
0.09756098 0.29268293 0.29268293 0.31707317
0.14285714 0.11904762 0.11904762 0.61904762
0.05000000 0.17500000 0.12500000 0.65000000
0.11904762 0.07142857 0.19047619 0.61904762
0.17948718 0.25641026 0.17948718 0.38461538
0.15384615 0.56410256 0.07692308 0.20512821
0.15000000 0.27500000 0.20000000 0.37500000
0.10000000 0.27500000 0.27500000 0.35000000
0.30769231 0.25641026 0.12820513 0.30769231
0.22500000 0.42500000 0.27500000 0.07500000
0.11904762 0.14285714 0.04761905 0.69047619
0.04761905 0.00000000 0.80952381 0.14285714
0.00000000 0.02380952 0.85714286 0.11904762

MOTIF elt-2
letter-probability matrix alength=4 w=10
0.74 0.04 0.13 0.09
0.28 0.29 0.13 0.31
0.07 0.08 0.08 0.91
0.00 0.00 1.00 0.00
1.00 0.00 0.00 0.00
0.00 0.00 0.00 1.00
1.00 0.00 0.00 0.00
0.97 0.00 0.02 0.01
0.19 0.15 0.53 0.13
0.54 0.09 0.20 0.17

MOTIF mab-3
letter-probability matrix alength=4 w=13 nsites=100
0.0800000 0.0300000 0.1300000 0.7600000
0.1400000 0.0000000 0.0000000 0.8600000
0.9900000 0.0100000 0.0000000 0.0000000
0.0000000 0.0000000 1.0000000 0.0000000
1.0000000 0.0000000 0.0000000 0.0000000
1.0000000 0.0000000 0.0000000 0.0000000
0.0000000 0.0000000 1.0000000 0.0000000
0.0000000 1.0000000 0.0000000 0.0000000
0.0100000 0.1900000 0.6700000 0.1300000
0.2700000 0.0000000 0.1100000 0.6200000
0.4400000 0.0000000 0.0600000 0.5000000
0.3469388 0.1326531 0.2244898 0.2959184
0.7400000 0.0800000 0.1000000 0.0800000

The error I get is as follows:

The output from your job will be found here: http://nbcr-222.ucsd.edu/opal-jobs/appMAST_4.9.01383184324959731760394

The following information may help your system administrator solve the problem

Message: Execution failed - process exited with value 1
Output code: 4

---

MAST Job - Error

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Results

• Input Motifs
• Uploaded Input Sequences
• Error Messages

Status Messages

• Parsing arguments
• Arguments ok
• Starting mast
  mast Known_Gut_PWMs_meme_final.txt 13578.Embryo.ce10.footprints.slop10.fa -oc . -nostatus -remcorr -ev 10
• mast exited with error code 1

FATAL: Motif with no PSPM or PSSM should not get here!

I would appreciate any advice. Many thanks in advance,

Margaret Ho
Graduate Student at Caltech

[James Johnson]

Hi Margaret,

Sorry for the delay in authorizing this post - I had forgotten to check the forums.

I see Charles has already answered this on the mailing list so I'm reposting Charles's answer here in case it's of use to anyone else.

It looks like you have several typos in your motifs that keep MAST from being able to parse the file.
We've tried to make the motif file parser reasonably flexible, but there are some bits of text in the
file that we use as landmarks and they have to exactly match the expected value.

I've marked the typos below:

MOTIF skn-1
letter-probability matrix alength=4 w=12 nsites=33

This should be: 

letter-probability matrix: alength=4 w=12 nsites=33 

Note the ':' after 'matrix'

0.18939394 0.37121212 0.09848485 0.3409091
0.51515152 0.12121212 0.06060606 0.3030303
0.42424242 0.06060606 0.09090909 0.4242424
0.21969697 0.09848485 0.03787879 0.6439394
0.42424242 0.00000000 0.57575758 0.0000000
0.00000000 0.00000000 0.00000000 1.0000000
0.00000000 1.00000000 0.00000000 0.0000000
1.00000000 0.00000000 0.00000000 0.0000000
0.00000000 0.00000000 0.00000000 1.0000000
0.03030303 0.45454545 0.27272727 0.2424242
0.39393939 0.36363636 0.06060606 0.1818182
0.36363636 0.21212121 0.06060606 0.3636364

MOTIF tra-1 letter-probability matrix alength=4 w=23 nsites=42

Missing the ':' here too. It also looks like w=13, not w=23, so the line should be:
letter-probability matrix: alength=4 w=13 nsites=42

0.09756098 0.29268293 0.29268293 0.31707317
0.14285714 0.11904762 0.11904762 0.61904762
0.05000000 0.17500000 0.12500000 0.65000000
0.11904762 0.07142857 0.19047619 0.61904762
0.17948718 0.25641026 0.17948718 0.38461538
0.15384615 0.56410256 0.07692308 0.20512821
0.15000000 0.27500000 0.20000000 0.37500000
0.10000000 0.27500000 0.27500000 0.35000000
0.30769231 0.25641026 0.12820513 0.30769231
0.22500000 0.42500000 0.27500000 0.07500000
0.11904762 0.14285714 0.04761905 0.69047619
0.04761905 0.00000000 0.80952381 0.14285714
0.00000000 0.02380952 0.85714286 0.11904762

MOTIF elt-2

letter-probability matrix alength=4 w=10

Missing the ':" here too.

0.74 0.04 0.13 0.09
0.28 0.29 0.13 0.31
0.07 0.08 0.08 0.91

The row above doesn't sum to 1.0. Each of the rows in the PSPM has to sum to 1.

0.00 0.00 1.00 0.00
1.00 0.00 0.00 0.00
0.00 0.00 0.00 1.00
1.00 0.00 0.00 0.00
0.97 0.00 0.02 0.01
0.19 0.15 0.53 0.13
0.54 0.09 0.20 0.17

MOTIF mab-3
letter-probability matrix alength=4 w=13 nsites=100

Missing ':' here too.

If you fix those typos MAST is able to process the file.