maffiter with compression file error

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于振朋

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Jun 27, 2020, 12:49:00 AM6/27/20
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my command as follow:

input.file=all.chr3.maf.gz //Input maf file
input.file.compression=gzip
input.format=Maf
input.dots=as_gaps


maf.filter=  \
RemoveEmptySequences(unresolved_as_gaps=yes),        \
Subset(                                 \
        species=(hg38,acol,agaz,bacu,bmus,btau,bwha,cdro,cfam,chir,curs,dleu,ejub,fcat,gmel,hm,lafr,lobl,lvex,lwed,mmon,mmus,mnov,nasi,nsch,odiv,oorc,pcat,pdis,plar,psin,pvit,schi,sscr,tadu,tlat,ttru,zcal), \
        strict=yes,                         \
        keep=no,                            \
        remove_duplicates=yes),             \
Merge(                                  \
        species=(hg38), \
        dist_max=0),                       \
Output(\
file=all.chr3.filtered.maf,\
compression=none,\
mask=no)

But I get error:
******************************************************************
*                  MAF Filter, version 1.3.1                     *
* Author: J. Dutheil                        Created on  10/09/10 *
*                                           Last Modif. 18/08/18 *
******************************************************************

Parsing options:
Parsing file maffilter_param.txt for options.
Segmentation fault (core dumped)


Could you give me some help.

Julien Y. Dutheil

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Jun 27, 2020, 2:09:10 AM6/27/20
to MafFilter
Hi,

In order to check what is going on, I would need your input file (or a minimal version allowing to reproduce the error). Would you mind sharing it so that I give it a look?

Best regards,

Julien.

于振朋

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Jun 28, 2020, 12:27:07 AM6/28/20
to MafFilter
Command show as follow.

input.file=hg38_ref.maf.gz //Input maf file
input.file.compression=gzip
input.format=Maf
input.dots=as_gaps
input.check_sequence_size=true


maf.filter=  \
RemoveEmptySequences(unresolved_as_gaps=yes),        \
Subset(                                 \
        species=(hg38,acol,agaz,bacu,bmus,btau,bwha,cdro,cfam,chir,curs,dleu,ejub,fcat,gmel,hm,lafr,lobl,lvex,lwed,mmon,mmus,mnov,nasi,nsch,odiv,oorc,pcat,pdis,plar,psin,pvit,schi,sscr,tadu,tlat,ttru,zcal), \
        strict=yes,                         \
        keep=no,                            \
        remove_duplicates=yes),             \
Merge(                                  \
        species=(hg38), \
        dist_max=0,                       \
ignore_chr=(Random,Unknown),        \
rename_chimeric_chromosomes=yes),   \
Output(\
file=all.chrY.filtered.maf,\
compression=none,\
mask=no)

Julien Y. Dutheil

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Jun 28, 2020, 1:35:47 AM6/28/20
to MafFilter
Hi,

I tried the input and option files, and it worked without error for me. May I ask which version of MafFilter you are using, on which OS and how you installed it? (from source, binary, ...)

Best regards,

Julien.

于振朋

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Jun 28, 2020, 4:08:09 AM6/28/20
to MafFilter
the Maffilter version is 1.3.1. I installed it on centos6.9 from source.

Julien Y. Dutheil

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Jun 28, 2020, 3:52:38 PM6/28/20
to MafFilter
Which version of the Bio++ libraries did you use (and how did you install them) ?
In case, I have uploaded a standalone Linux binary executable https://github.com/jydu/maffilter/releases/tag/v1.3.1 . It was generated on Linux ubuntu, but should hopefully work out of the box... would you mind giving it a try?

Best regards,

Julien.

zhenpeng yu

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May 26, 2022, 1:19:11 PM5/26/22
to MafFilter
The MAFs should be sort by maf_sort.
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