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.
•
written
by
kamynz16 •
The error message is Segmentation fault (core dumped).
The bug error report as suggested in Bwa Index Segmentation Fault
Command:
/datos-biologia2/BioProgs_SGE/bin/muscle -in XsPaperBSR_tblastx.orth/Sboy:487.fasta -quiet -out XsPaperBSR_tblastx.aln/Sboy:487.aln
I did some research of this error message but I still don't understand what exactly means.
•
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kamynz16 •
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
OK. Thanks, I'll see if that works.
•
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kamynz16 •
Hi Philipp,
I use the newest version of muscle (3.8.31), and it is working. Thanks for the help.
•
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kamynz16 •
Great to hear, good luck!
Log in to answer this question.
In your MUSCLE command, it looks like you throw away the actual error message by piping it into
/dev/null:What is the error message when you pipe that into a file?
Edit: You might also want to replace
-quietby-verbose -log log_file.txtto get a better handle on what's actually happening