Re: [Mapass-help] sh: line 1: 6472 Segment default

[Heng Li <lh...@gm...>]

Well, it is me...

I guess there is not enough memory to do this in one go. You can =20
separate your reads into, say 5, separate files, and run as:

mapass2.pl easyrun -d test reference.fa seq*.fastq

Heng


On 15 Jun 2007, at 09:57, Liu Tao wrote:

> Hi, mapass-admin:
>
>  When I run mapass2, using the command:
>
>       mapass2.pl easyrun -d assembly_rst reference.fa =20
> sequence_rst.fastq
>
>  Because of my misunderstanding of the introduction of fastq's =20
> format. I got the following errors:
>
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D
> [easyrun] Converting the reference sequence 'reference.fa' to =20
> binary fasta format (.bfa)...
> 89 sequences have been converted.
> [easyrun] Converting fastq file 'sequence_rst.fastq' to binary =20
> fastq format (.bfq)...
> 2463084 sequences were loaded.
> [easyrun] Aligning reads-1.bfq to the reference...
> [ma_load_reads] loading reads...
> [ma_load_reads] set length of the first read as 33.
> [ma_load_reads] 2463084*2 reads loaded.
> [ma_longread2read] encoding reads... 4926168 sequences processed.
> [match_core] round 1/3...
> [match_core] making index..
> sh: line 1:  6472 Segmentation fault      /usr/local/bin/mapass2 =20
> match reads-1.map ref.bfa reads-1.bfq
> Died at /usr/local/bin/mapass2.pl line 109.
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
>
> My fault is : the quality of the sequence was converted by the code
> you pubilished on the home site of mapass:
>
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
> my $std_qseq =3D '';
> while ($sol_qseq =3D~ /(\S)/g) {
> $std_qseq .=3D chr(int(33 + 10*log(1+pow(10,(ord($1)-64)/10.0))/log=20
> (10)+.499));
> }
>
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
> It may be not a bug of program though, supply it here to let you =20
> know that
> it will report the imformation above, and the reason is ambiguous.
>
> And now I have corrected the error, then go through the program and =20=

> get some assemblies.
> The result seems good.
>
> I'd glad to help to improve this project. Thank you.
>
> Best Regards!
> Liu Tao
>
>
> 150 =E4=B8=87 =E4=BA=BA =E5=90=8C =E6=97=B6 =E5=9C=A8 =E7=8E=A9 =E7=9A=84=
 =E7=BD=91 =E6=B8=B8=EF=BC=8C=E4=BD=A0 =E4=B8=8D =E8=AF=95 =E8=AF=95 =E5=90=
=97 =EF=BC=9F
> ----------------------------------------------------------------------=20=

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