Re: [wgs-assembler-users] problem with celera 7.0 and amos 3.1.0

[Serge K. <se...@um...>]

Yes, Jared is correct. You need to use gatekeeper to cerate the frg file. CA renames the sequences from a fastq file which is why you are getting the error about undefined fragments. Dumping the frg file from the gatekeeper will get the correct names. cavalidate will run toAmos and other scripts to create your bank. toAmos_new is recommended for larger projects as it is significantly faster than toAmos.

Sergey

On Aug 28, 2013, at 10:28 PM, "Decker, Jared Egan (MU-Student)" <je...@ma...> wrote:

> Diego,
> First I would run this:
> gatekeeper -dumpfrg PROJECT.gkpStore | grep -v 'No source' > PROJECT.frg
> In your case, it looks like SE-MT8 is your PROJECT prefix.
> Then run
> cavalidate PROJECT
> with your PROJECT prefix. This will create a bank that you can analyze with FRCurve and Hawkeye.
>  
> If I am off base, hopefully one of the other list serve members can straighten me out. :-)
>  
> Thanks,
> Jared
>  
> Jared Decker
> Assistant Professor, Beef Genetics Extension and Computational Genomics
> Division of Animal Sciences
> University of Missouri
> S132B ASRC
> 920 East Campus Dr.
> Columbia, MO 65211
> Phone 573-882-2504
> http://www.linkedin.com/in/jarededecker 
>  
>  
>  
> From: diego [mailto:die...@gm...] 
> Sent: Wednesday, August 28, 2013 5:30 PM
> To: wgs...@li...
> Subject: [wgs-assembler-users] problem with celera 7.0 and amos 3.1.0
>  
> Hi
> 
> I'm trying to visualize my celera assembly with Hawkeye, but i get an error when i use toAmos script to parse my .asm file.
> 
> I tried with two scripts, "toAmos" and "toAmos_new", but i get similar errors.
> 
> Error with toAmos
> "$toAmos -f ../C28.frg  -a SE-MT8.asm -o - | bank-transcat -m - -b example.bnk -c
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133168.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133175.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133182.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133189.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133196.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133203.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133210.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133217.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133224.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133231.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133238.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133245.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133252.
> Use of uninitialized value $iid in hash element at /projects3/ddiaz/amos/bin/toAmos line 1274, <IN> line 133259.
> .."
> 
> i checked the line 1274 on toAmos script and it has the following sentence: " $seq_range{$iid} = $clrstr;".
> This error arises from previous line "my $iid = $seqids{$acc};" where $seqids{$acc} is null.
> I noticed that "$seqids{$acc}" is filled up on the sub "parseFrgFile", on the following sentence: 
> 
> "  if ($type eq "FRG") {
>             my $id = getCAId($$fields{acc});
>             my $iid = $minSeqId++;
>             my $nm = $$fields{src};
>             my @lines = split('\n', $nm);
>             $nm = $lines[0]; # join('', @lines);
>             if ($byaccession || !defined $nm || $nm =~ /^\s*$/) {
>                 $seqnames{$iid} = $id;
>             } else {
>                 $seqnames{$iid} = $nm;
>                 $seqids{$nm} = $iid;
>             }
>             $seqids{$id} = $iid;"
> 
> but there isn't any FRG string on the .asm file.
> 
> Error with toAmos_new
> "$ toAmos_new ../data/trimmomatic_outputs/Vpkx_unmated.frg -a SE-MP-3.4.asm -b Vpkx.bank"
> Error fragments 110000762732 are not defined
> Error fragments 110000596019 are not defined
> Error fragments 120000810529 are not defined
> Error fragments 200001924304 are not defined
> Error fragments 200001469500 are not defined
> Error fragments 200001648709 are not defined
> Error fragments 110000674424 are not defined
> Error fragments 110001085229 are not defined
> Error fragments 200001936657 are not defined
> Error fragments 110001088561 are not defined
> Error fragments 120001030615 are not defined
> Error fragments 120000286346 are not defined
> ...."
> 
> It believe this it's similar to previous error, due to the absence of the FRG string on the .asm output, i think.
> Despite this, i can get the fasta file with contigs and scaffolds of my assembly.
> 
> First, I used sff_extract script to get fastq files, then , i converted this files to celera inputs with the fastqtoCA and finally, i executed celera.
> 
> Could someone help me with this please? 
> 
> i need to transform my celera outputs to AMOS bank to analyze it with Hawkeye.
> 
> Thanks in advance!
> 
> PD: sorry for my English.
> Diego Díaz.
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