data input error

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Kuselah Tayaban

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Jun 6, 2020, 3:39:51 AM6/6/20
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Hello all,

I'm using iq-tree for the first time. I have a sequence alignment in fasta format for reconstructing ML tree, but as I run it in iq-tree using the command iqtree -s gcspp.fas, it gives an error like this:
Reading alignment file gcspp.fas ... ERROR: Cannot read file gcspp.fas

I also tried it with phylip format, but still gives the same error. My sequences have same lengths, so what would be the possible problem? Sorry I can't find any answer/solution in the documentation online. Hope you guys can help...

Thanks!

Rob Lanfear

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Jun 8, 2020, 8:17:50 PM6/8/20
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Hi Kuselah,

It sounds like there is an error in your alignment file. If you can post the file here then we can take a look and advise. An example of an aligned fasta file is here:

Rob

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Rob Lanfear
Division of Ecology and Evolution,
Research School of Biology,
The Australian National University,
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Minh Bui

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Jun 8, 2020, 8:57:43 PM6/8/20
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Or perhaps because you ran IQ-TREE in a different folder, where this alignment does not exist?

Minh

Kuselah Tayaban

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Jun 9, 2020, 1:12:29 AM6/9/20
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Hi Rob,

Here is my fasta file. Thanks for taking a look.

Best,
Kuselah


On Tuesday, June 9, 2020 at 8:17:50 AM UTC+8, Rob Lanfear wrote:
Hi Kuselah,

It sounds like there is an error in your alignment file. If you can post the file here then we can take a look and advise. An example of an aligned fasta file is here:

Rob

On Sat, 6 Jun 2020 at 17:39, Kuselah Tayaban <kmta...@gmail.com> wrote:
Hello all,

I'm using iq-tree for the first time. I have a sequence alignment in fasta format for reconstructing ML tree, but as I run it in iq-tree using the command iqtree -s gcspp.fas, it gives an error like this:
Reading alignment file gcspp.fas ... ERROR: Cannot read file gcspp.fas

I also tried it with phylip format, but still gives the same error. My sequences have same lengths, so what would be the possible problem? Sorry I can't find any answer/solution in the documentation online. Hope you guys can help...

Thanks!

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gcspp.fas

Kuselah Tayaban

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Jun 9, 2020, 1:14:07 AM6/9/20
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Hi Minh,

I'm in the right folder. If the file is in a different folder, the error would be "file does not exist", wouldn't it be?

Thanks a lot,
Kuselah


On Tuesday, June 9, 2020 at 8:57:43 AM UTC+8, Minh Bui wrote:
Or perhaps because you ran IQ-TREE in a different folder, where this alignment does not exist?

Minh

On 9 Jun 2020, at 10:17 am, Rob Lanfear <rob.l...@gmail.com> wrote:

Hi Kuselah,

It sounds like there is an error in your alignment file. If you can post the file here then we can take a look and advise. An example of an aligned fasta file is here:

Rob

On Sat, 6 Jun 2020 at 17:39, Kuselah Tayaban <kmta...@gmail.com> wrote:
Hello all,

I'm using iq-tree for the first time. I have a sequence alignment in fasta format for reconstructing ML tree, but as I run it in iq-tree using the command iqtree -s gcspp.fas, it gives an error like this:
Reading alignment file gcspp.fas ... ERROR: Cannot read file gcspp.fas

I also tried it with phylip format, but still gives the same error. My sequences have same lengths, so what would be the possible problem? Sorry I can't find any answer/solution in the documentation online. Hope you guys can help...

Thanks!

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Rob Lanfear
Division of Ecology and Evolution,
Research School of Biology,
The Australian National University,
Canberra

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Minh Bui

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Jun 9, 2020, 3:35:28 AM6/9/20
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It works just fine in my laptop (MacBook):

...
Reading alignment file gcspp.fas ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 134 sequences with 204 columns, 124 distinct patterns
55 parsimony-informative, 33 singleton sites, 116 constant sites

So no idea what happened… which OS are you running? Mac, Windows, or Linux?

Perhaps it has something to do with the file system, e.g. check the file permission.

Minh

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Kuselah Tayaban

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Jun 9, 2020, 3:57:24 AM6/9/20
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Hi Minh,

I forgot to check file permission. It already worked!

Thanks a lot,
Kuselah
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