[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.

[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

[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

[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.

[condomitti]

Hi Boetsie,

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

Thank you very much!

Best rgrds,
Conomitti.

[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]

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.

[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?

[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

[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 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

[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

[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..

[NGS group]

Is that possible to use already paired library for SSPACE

Hi all,

We normally use CLC bio for assembly, and CLC bio always pair the two Reads into one (i.e. R1.fastq + R2.fastq = pair.fastq).

However, in the SSPACE tutorial, the two Reads should be listed separately in the "library file" as: Lib1 bwa R1.fastq R2.fastq 4000 0.5 RF

Therefore, I would like to ask whether I could change the "library file" as:
Lib1 bwa pair.fastq 4000 0.5 RF

In addition, it seems that untrimmed reads could give better results than trimmed results. Do you trim your reads before running SSPACE?

Thank you for your helps in advance!

Cheers,

Kai

[NGS group]

waiting................