[rhinoceros]

Hi Amery, sorry just saw your question now, the good news is yes I solve it but the bad news is that the solution was running it with only one processor. I would love to know if you could also solve it by other way, because it takes ages running it with only one thread.

Cheers

L

Just reporting the same problem with SSPACE_Standard_v3.0, but only when "-x 1". "-T 1" didn't fix it for me. Could the problem be in ExtendOrFormatContigs.pl if statements?

if($#filesbowtie >[B]=[/B] 0)
..
if($#filesbwa >[B]=[/B] 0 || $#filesbwasw >[B]=[/B] 0){

Shouldn't these be ">=1" or ">0"? The program finishes just fine if I use bwa or bwasw instead of bowtie..

[rotblaugelb]

hi boetsie,

i just stumbled across your program and would like to use it.
for the read libraries, how are they build? could you give an example of the steps to get there? i have read files in fastq format let's say R1.fastq and R2.fastq

thanks, julia

[luiscunhamx]

Hi Amery, sorry just saw your question now, the good news is yes I solve it but the bad news is that the solution was running it with only one processor. I would love to know if you could also solve it by other way, because it takes ages running it with only one thread.

Cheers

L

[duxingxia]

Hi Boetsie

Hi hope you can help me. I have been trying to use sspace to scaffold a old assembly with a new paired end library, several times, using different parameters and keeps giving the following error:
"Thread 26 terminated abnormally: Can't open bwa output -- fatal"

Although in my library file I have bowtie as selected aligner

"lib1 bowtie ../corrected_trimmomatic_rubellus_1.fastq.gz ../corrected_trimmomatic_rubellus_2.fastq.gz 225 0.60 FR"

The last log message is that is doing the mapping stage

"2014: Mapping reads to contigs with Bowtie"

and that's it,

Can you please advise me where to look in order to try track the issue?

Thanking in advance

Luis

I have same problem. Have you solved the problem, Luis?

Amery

[luiscunhamx]

Hi Boetsie

Hi hope you can help me. I have been trying to use sspace to scaffold a old assembly with a new paired end library, several times, using different parameters and keeps giving the following error:
"Thread 26 terminated abnormally: Can't open bwa output -- fatal"

Although in my library file I have bowtie as selected aligner

"lib1 bowtie ../corrected_trimmomatic_rubellus_1.fastq.gz ../corrected_trimmomatic_rubellus_2.fastq.gz 225 0.60 FR"

The last log message is that is doing the mapping stage

"2014: Mapping reads to contigs with Bowtie"

and that's it,

Can you please advise me where to look in order to try track the issue?

Thanking in advance

Luis

[ret4andry]

I'd still like to use 454 PE data to scaffold my assembly. Is there some intermediate file or Bowtie like PE format that we can feed to SSPACE?

[condomitti]

Sorry for the late reply. It seems that I do not get an e-mail notification anymore when a reply is given in this thread

Please have a look at this post where colindaven suggests how to fix the problem;

http://seqanswers.com/forums/showpost.php?p=81988&postcount=150

Boetsie

Thanks Boetsie! That seems to solve!!

Cheers,
Condomitti.

[boetsie]

Sorry for the late reply. It seems that I do not get an e-mail notification anymore when a reply is given in this thread

Please have a look at this post where colindaven suggests how to fix the problem;

http://seqanswers.com/forums/showpost.php?p=81988&postcount=150

Boetsie

Hi Boetsie,

Do you have a clue on how I could find out about that error?

Thank you very much!

Best rgrds,
Conomitti.

[condomitti]

Hi Boetsie,

Do you have a clue on how I could find out about that error?

Thank you very much!

Best rgrds,
Conomitti.

[condomitti]

Hello fellows,

I've been trying to assemble pre-assembled contigs into scaffolds using SSPACE. Everything goes ok up to a specific point where the software stops and gives me the following message:

Bowtie-build error; -1 at /usr/local/src/sspace-basic/bin/PairingAndScaffolding.pl line 829.

I tried running with -v option but no extra messages are output.
Could please someone give me some help on how to debug that issue?

I'm using a single fastq file of pre-assembled contigs and enabling contig extension ( -x 1 ) option, which should use a set of mate-pair reads I'm passing in on libraries.txt file.


Thanks a lot.

Cheers,
George Condomitti.

[DAPOR]

Hi Anna,

How did you solve the problem with "Can't locate getopts.pl in @INC (@INC contains"
I can't figure it out

Thanks

[maubp]

yes, this is possible. The file should be in a TAB delimited format like:

<contig1> <startpos_on_contig1> <endpos_on_contig1> <contig2> <startpos_on_contig2> <endpos_on_contig2>

E.g.
contig1 100 150 contig1 350 300
contig1 4000 4050 contig2 110 60

There is a script in the 'tools' directory of the package to convert SAM/BAM to a tab format.

Regards,
Boetsie

Where should we report SSPACE bugs? The tools/sam_bam2Tab.pl script included in SSPACE basic v2.0 is extremely brittle - it cannot handle properly formatted paired end SAM/BAM (using the FLAG field), and instead expects fake single read data with read suffices (and only looks at the reverse complement bit of the FLAG). Thanks.

Update: I've started hacking together a Python replacement https://github.com/peterjc/picobio/b..._sspace_tab.py

[cronopio]

Hi Boetsie,

I've tried to run the SSPACE example (E. Coli, contigs_abyss.fasta, etc.) in order to test the program.
I follow all the steps, but the final result is a file with 111 scaffolds. Why is that? I was supposed to get only a few scaffolds, isn't?

Could you please give me some advices? I don't know what I'm doing wrong.

Thank you very much.
Germán.

[xuseq]

Hi, Anna

That's right! Thank you!

Xu,

Have you specified the output directory in your command line?
If yes - delete it.

[OTU]

Xu,

Have you specified the output directory in your command line?
If yes - delete it.