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pangenome / maffer

extract MSAs from genome variation graphs
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maffer did not accept the new version of xg from vg indexed graph .xg #4

Open XuewenWangUGA opened 3 years ago

XuewenWangUGA commented 3 years ago

I try to convert the xg from vg version 1.24 to maf using Maffer. However, the maffter reported that the xg version is too new to ba accepted. Is it possible to update the maffer?

input: vg indexed graph file .xg Error information: bash ./vg_maffer.sh warning [libhandlegraph]: Serialized handle graph does not appear to match deserialzation type. warning [libhandlegraph]: It is either an old version or in the wrong format. warning [libhandlegraph]: Attempting to load it anyway. Future releases will reject it! terminate called after throwing an instance of 'xg::XGFormatError' what(): XG index file version 3909550680 is too new to interpret (max version = 14) ./vg_maffer.sh: line 64: 14220 Aborted (core dumped) $toodir/maffer -i $inf -t $nthreadxw > $otmaf

ekg commented 3 years ago

Ouch. I would suggest using pggb (smoothxg in particular) to obtain a MAF file for the pangenome.

It takes GFA as input, avoiding the incompatibility.

On Tue, Oct 27, 2020 at 6:48 PM XuewenWangUGA notifications@github.com wrote:

I try to convert the xg from vg version 1.24 to maf using Maffer. However, the maffter reported that the xg version is too new to ba accepted. Is it possible to update the maffer?

input: vg indexed graph file .xg Error information: bash ./vg_maffer.sh warning [libhandlegraph]: Serialized handle graph does not appear to match deserialzation type. warning [libhandlegraph]: It is either an old version or in the wrong format. warning [libhandlegraph]: Attempting to load it anyway. Future releases will reject it! terminate called after throwing an instance of 'xg::XGFormatError' what(): XG index file version 3909550680 is too new to interpret (max version = 14) ./vg_maffer.sh: line 64: 14220 Aborted (core dumped) $toodir/maffer -i $inf -t $nthreadxw > $otmaf

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ekg commented 3 years ago

It also correctly implements the MSA concept. Maffer is deprecated.

On Tue, Oct 27, 2020 at 7:05 PM Erik Garrison erik.garrison@gmail.com wrote:

Ouch. I would suggest using pggb (smoothxg in particular) to obtain a MAF file for the pangenome.

It takes GFA as input, avoiding the incompatibility.

On Tue, Oct 27, 2020 at 6:48 PM XuewenWangUGA notifications@github.com wrote:

I try to convert the xg from vg version 1.24 to maf using Maffer. However, the maffter reported that the xg version is too new to ba accepted. Is it possible to update the maffer?

input: vg indexed graph file .xg Error information: bash ./vg_maffer.sh warning [libhandlegraph]: Serialized handle graph does not appear to match deserialzation type. warning [libhandlegraph]: It is either an old version or in the wrong format. warning [libhandlegraph]: Attempting to load it anyway. Future releases will reject it! terminate called after throwing an instance of 'xg::XGFormatError' what(): XG index file version 3909550680 is too new to interpret (max version = 14) ./vg_maffer.sh: line 64: 14220 Aborted (core dumped) $toodir/maffer -i $inf -t $nthreadxw > $otmaf

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XuewenWangUGA commented 3 years ago

Erik, Thanks for letting me know.

Xuewen

From: Erik Garrison notifications@github.com Sent: Tuesday, October 27, 2020 2:12 PM To: pangenome/maffer maffer@noreply.github.com Cc: Xuewen Wang xwwang@uga.edu; Author author@noreply.github.com Subject: Re: [pangenome/maffer] maffer did not accept the new version of xg from vg indexed graph .xg (#4)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Ouch. I would suggest using pggb (smoothxg in particular) to obtain a MAF file for the pangenome.

It takes GFA as input, avoiding the incompatibility.

On Tue, Oct 27, 2020 at 6:48 PM XuewenWangUGA notifications@github.com wrote:

I try to convert the xg from vg version 1.24 to maf using Maffer. However, the maffter reported that the xg version is too new to ba accepted. Is it possible to update the maffer?

input: vg indexed graph file .xg Error information: bash ./vg_maffer.sh warning [libhandlegraph]: Serialized handle graph does not appear to match deserialzation type. warning [libhandlegraph]: It is either an old version or in the wrong format. warning [libhandlegraph]: Attempting to load it anyway. Future releases will reject it! terminate called after throwing an instance of 'xg::XGFormatError' what(): XG index file version 3909550680 is too new to interpret (max version = 14) ./vg_maffer.sh: line 64: 14220 Aborted (core dumped) $toodir/maffer -i $inf -t $nthreadxw > $otmaf

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