Question: Velvet Postprocessing
1
gravatar for khikho
8.9 years ago by
khikho100
GermanyLeipzig
khikho100 wrote:

when I run Postprocessor script (version 1.6 ) on my contigs (make them by velvet) I got these errors with tones of repeats , could you give me hint to handle these errors!?

I don't know which info should I give to make the situation clear so ask me what ever makes it more clear for you!?

Use of uninitialized value $seq_id in print at Package/denovo_postprocessor_solid_v1.6.pl line 243, <OUT> line 272998.Use of uninitialized value $seq_id in split at Package/denovo_postprocessor_solid_v1.6.pl line 245, <OUT> line 272998.Use of uninitialized value $seq in split at Package/denovo_postprocessor_solid_v1.6.pl line 272, <OUT> line 272998.Use of uninitialized value $seq_id in string at Package/denovo_postprocessor_solid_v1.6.pl line 342, <OUT> line 272998.Use of uninitialized value $seq in concatenation (.) or string at Package/denovo_postprocessor_solid_v1.6.pl line 343, <OUT> line 272998.format of input wrong

BTW I plan to assemble human genome.

Thanks

assembly next-gen solid velvet • 1.6k views
ADD COMMENTlink written 8.9 years ago by khikho100

it seems that you are using the color space pipeline from SOLiD make sure you have the right version of tools, perl etc installed. In my experience with older version of the color space assembly pipeline is that the scripts should at least work right out of the package

ADD REPLYlink written 8.9 years ago by Istvan Albert ♦♦ 86k

Yes I use color space data and all of the tools which I use are updated , so I don't know where this error comes from!? But tmp folder which is used by postprocessor_solid won't be free and It's fishy.

ADD REPLYlink written 8.9 years ago by khikho100

"I plan to assemble human genome."
I think the SOLiD reads will make this plan close to impossible...

ADD REPLYlink written 8.4 years ago by Torst960
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