Can MUSCLE work with small sequences? MSG: Muscle call crashed: 512

Question

[kamynz16]

Hi all,

I'm having trouble with the same error while running MUSCLE in Unus that is a Perl package for phylogenomic analyses.

Error message:

WARNING ---------------------

MSG: Muscle call crashed: 512 [command /datos-biologia2/BioProgs_SGE/bin/muscle -in XsPaperBSR_tblastx.orth/Sboy:487.fasta -quiet -out XsPaperBSR_tblastx.aln/Sboy:487.aln 2> /dev/null]

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

This message appears 19 times and with sequences that are small, such as:

>Sboy:487
GTGATACAGCGCCAGACAAATGGCGTCCAGCAGGGTGGTTTTCCCCGCACCGGTTGGGCC
GGTAATGGCAAACAGCCCGTTGCTGGCGAACGGCTCGCGGGTGAAATCAATCTTCCATTC
GCCTTTTAA

When Unus is trying to do the multiple alignment of a group of orthologos, such as:

>Sboy:487
GTGATACAGCGCCAGACAAATGGCGTCCAGCAGGGTGGTTTTCCCCGCACCGGTTGGGCC
GGTAATGGCAAACAGCCCGTTGCTGGCGAACGGCTCGCGGGTGAAATCAATCTTCCATTC
GCCTTTTAA
>Sdys:597
ATGAAAATTCTCAGCCTGCGCCTGAAAAACCTGAACTCATTAAAAGGCGAATGGAAGATT
GATTTCACCCGCGAGCCGTTCGCCAGCAACGGGCTGTTTGCAATTACCGGCCCAACCGGT
GCGGGGAAAACCACCCTGCTGGACGCCATTTGTCTGGCGCTGTATCACGAAACTCCGCGT
CTCTCTAACGTTTCACAATCGCAAAATGATCTCATGACCCGCGATACCGCCGAATGTCTG
GCGGAGGTGGAGTTTGAAGTGAAAGGTGAAGCGTATCGCGCGTTCTGGAGCCAGAATCGG
GCGCGTAACCAACCCGACGGTAATTTGCAGGTGCCACGCGTAGAGCTGGCGCGCTGCGCC
GACGGCAAAATTCTCGCCGACAAAGTGAAAGATAAGCTGGAACTGACAGCGACGTTAACC
GGGCTGGATTACGGGCGCTTCACCCGTTCGATGCTGCTTTCGCAGGGGCAATTTGCTGCC
TTCCTGAATGCCAAACCCAAAGAACGCGCGGAATTGCTCGAGGAGTTAACCGGCACTGAA
ATCTACGGGCAAATCTCGGCGATGGTTTTTGAGCAGCACAAATCGGCCCGCACTGAGCTG
GAGAAGCTGCAAGCGCAGGCCAGCGGCGTCGCGTTGCTCACGCCGGAACAAGTGCAATCG
CTGAAAGCGAGTTTGCAGGTACTTACTGACGAAGAAAAACTGTTACTTACCGCGCAGCAG
CAAGAACAACAATCACTAAACTGGTTAACGCGTCTGGACGAATTGCAGCAAGAAGCCAGC
>Sfle:578
ATGAAAATTCTCAGCCTGCGCCTGAAAAACCTGAACTCATTAAAAGGCGAATGGAAGATT
GATTTCACCCGCGAGCCGTTCGCCAGCAACGGGCTGTTTGCCATTACCGGCCCAACCGGT
GCGGGGAAAACCACCCTGCTGGACGCCATTTGTCTGGCGCTGTATCACGAAACTCCGCGT
CTCTCTAACGTTTCACAATCGCAAAATGATCTCATGACCCGCGATACCGCTGAATGTCTG
GCGGAGGTGGAGTTTGAAGTGAAAGGTGAAGCGTATCGCGCGTTCTGGAGCCAGAATCGG
GCGCGTAACCAGCCGGACGGTAATTTGCAGGTGCCTCGCGTAGAGCTGGCGCGCTGCGCC
GACGGCAAAATTCTCGCCGACAAAGTGAAAGATAAGCTGGAACTGACAGCGACGTTAACC
GGGCTGGATTACGGGCGCTTCACCCGTTCGATGCTGCTTTCGCAGGGGCAATTTGCTGCC
TTCCTGAATGCCAAACCCAAAGAACGCGCGGAATTGCTCGAGGAGTTAACCGGCACTGAA
ATCTACGGGCAAATCTCGGCGATGGTTTTTGAGCAGCACAAATCGGCCCGCACTGAGCTG
GAGAAGCTGCAAGCGCAGGCCAGCGGCGTCACGTTGCTCACGCCGGAACAAGTGCAATCG
CTGACAGCGAGTTTGCAGGTACTTACTGACGAAGAAAAACAGTTAATTACCGCGCAGCAG
CAAGAACAACAATCGCTAAACTGGTTAACGCGTCAGGACGAATTGCAGCAAGAAGCCAGC
CGCCGTCAACAGGCCTTGCAACAGGCGTTAGCCGAAGAAGAAAAAGCGCAACCTCAACTG
GCGGCGCTTAGTCTGGCACAACCGGCACGAAATCTTCGTCCACACTGGGAACGCATCGCA
GAACACAGCGCGGCGCTGGCGCATATTCGCCAGCAGATTGAAGAAGTAAATACTCGCTTA
CAGAGCACAATGGCGCTTCGCGCGAGCATTCGCCACCACGCGGCGAAGCAGTCAGCAGAA
TTACAGCAGCAGCAACAAAGCCTGAATACCTGGTTACAGGAACACGACCGCTTCCGTCAG
TGGAACAACGAACTGGCGGGTTGGCGTGCGCAGTTCTCCCAACAAACCAGCGATCGCGAG
CATCTGCGGCAATGGCAGCAACAGTTAACCCATGCTGAGCAAAAACTTAATGCGCTTGCG
GCGATCACGTTGACGTTAACCGCCGATGAAGTTGCTACCGCCCTGGCGCAACATGCCGAG
CAACGCCCACTGCGTCAGCGCCTGGTCGCGCTGCATGGGCAGATTGTTCCCCAACAAAAA
CGTCTGGCGCAGTTAATGGTCACTATCCAGAATGTCACTCTGGAACAGACGCAACGTAAT
GTCGCACTTAACGAAATGCGCCAGCGTTATAAAGAAAAGACGCAGCAACTTGCCGATGTG

=> First, I thought that Muscle wasn't installed, but it is installed and can be found by Unus.

=> Second, I thought it was a memory problem but I submitted this job requesting a free_mem of 32G as the following:

#$ -l mem_free=32G,h_vmem=34G
#$ -pe make 8

Then, I'm desperate because I don't understand what is happening.

Should I eliminate the small sequences?

If somebody can help, I'll appreciate the help.

[Philipp Bayer]

In your MUSCLE command, it looks like you throw away the actual error message by piping it into /dev/null:

2> /dev/null

What is the error message when you pipe that into a file?

Edit: You might also want to replace -quiet by -verbose -log log_file.txt to get a better handle on what's actually happening

Answer 1

[kamynz16]

The error message is Segmentation fault (core dumped).

The bug error report as suggested in Bwa Index Segmentation Fault

1. MUSCLE (multiple sequence comparison by log-expectation). Version muscle3.5
2. Linux hellsgate 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux

3. Command:

   /datos-biologia2/BioProgs_SGE/bin/muscle -in XsPaperBSR_tblastx.orth/Sboy:487.fasta -quiet -out XsPaperBSR_tblastx.aln/Sboy:487.aln
   

4. Segmentation fault (core dumped)

I did some research of this error message but I still don't understand what exactly means.

[Philipp Bayer]

Segmentation faults are always a bit hard to debug... Usually, the easiest fix is to update your binary.

When you run MUSCLE without any arguments, what version does it report? I see you're running MUSCLE 3.5, the newest version is 3.8.31, try updating first

[kamynz16]

OK. Thanks, I'll see if that works.

[kamynz16]

Hi Philipp,

I use the newest version of muscle (3.8.31), and it is working. Thanks for the help.

[Philipp Bayer]

Great to hear, good luck!