[uloeber]

Hi all,
What am I doing wrong if I get:

READING READS lib1:
------------------------------------------------------------
Total inserted pairs = 3413702
Number of pairs containing N's = 17688
Remaining pairs = 3396014
------------------------------------------------------------



LIBRARY lib1 STATS:
################################################################################

MAPPING READS TO CONTIGS:
------------------------------------------------------------
Number of single reads found on contigs = 0
Number of pairs used for pairing contigs / total pairs = 0 / 0
------------------------------------------------------------

READ PAIRS STATS:
Assembled pairs: 0 (0 sequences)
Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 600 +/-60): 0
Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0
Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 0
---
Satisfied in distance/logic within a given contig pair (pre-scaffold): 0
Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 0
---
Total satisfied: 0 unsatisfied: 0


Estimated insert size statistics (based on 0 pairs):
Mean insert size = 0
Median insert size = 0
REPEATS:
Number of repeated edges = 0
------------------------------------------------------------
?
Thanks in advance!
Ulrike

[darthsequencer]

Hi - I have a question about the "-n" option.

Here's what the option does: "minimum overlap required between contigs to merge adjacent contigs"

Does this mean that the SSPACE will assemble to contigs together that have terminal overlaps - like minimus2 would do?

[sunnycqcn]

Usually, you can try a small dataset firstly.
Then software work well, you can run lots of data.
I am sure that my data run well now.

Hi sunnycqcn,

My libraries.txt file looks like the following:

gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
gjGA bowtie GerJamesonii_1_P.fastq GerJamesonii_2_P.fastq 125 0.25 FR


Thank you,

-Milo

[sunnycqcn]

How many libraries is in your libraries files.

Hi sunnycqcn,

My libraries.txt file looks like the following:

gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
gjGA bowtie GerJamesonii_1_P.fastq GerJamesonii_2_P.fastq 125 0.25 FR


Thank you,

-Milo

[milo0615]

I am sure the 3.0 version work well with the big genome. I assembled one genome last month, it worked well. Meanwhile, I met the same problem as same with you. So if your library file include a lot of libraries, the error file should be like as your error file. So if you can present your library file, I can know what it happen.

Hi sunnycqcn,

My libraries.txt file looks like the following:

gjHS bowtie GerJamesonii_HS_1_P.fastq GerJamesonii_HS_2_P.fastq 100 0.25 FR
gjGA bowtie GerJamesonii_1_P.fastq GerJamesonii_2_P.fastq 125 0.25 FR


Thank you,

-Milo

[El Crazy Xabi]

I found the SSPACE basic 2.1 in GitHub, from one of the original devs, so no need to bother with Baseclear to use the -x=1

https://github.com/nsoranzo/sspace_basic

[sunnycqcn]

I am sure the 3.0 version work well with the big genome. I assembled one genome last month, it worked well. Meanwhile, I met the same problem as same with you. So if your library file include a lot of libraries, the error file should be like as your error file. So if you can present your library file, I can know what it happen.

Hi fahmida,

If I use -x = 0 the assembly stats such as the N50, n>200, and max length stay the same. I have already emailed the SSPACE developers for an older version of it.

Thank you for your help.

-Milo

[milo0615]

Please see the response of 'El Crazy Xabi' above.
Either use -x = 0 or use an older version of SSPACE.

Hi fahmida,

If I use -x = 0 the assembly stats such as the N50, n>200, and max length stay the same. I have already emailed the SSPACE developers for an older version of it.

Thank you for your help.

-Milo

[fahmida]

Hi sunnycqcn,

The command I used is as follows. Thank you for your help

>perl $HOME/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s gercombsadaptrim200_k44-contigs.fa -x 1 -z 200 -T 16 -k 3 -a 0.7 -m 32 -r 0.9 -p 0 -o 15 -n 10 -v 1 -b gercombsk44 &

[1] 20196

log:

[stilllab@b30-fac-staff-134-71-20-58 NEW_SSPACE_Gerreg]$ Your inserted inputs on [SSPACE_Standard_v3.0_linux] at Mon Mar 7 15:40:17 2016:
Required inputs:
-l = libraries.txt
Number of paired files = 2
-s = gercombsadaptrim200_k44-contigs.fa
-b = gercombsk44

Optional inputs:
-x = 1
-z = 200
-k = 3
-g = 0
-a = 0.7
-n = 10
-T = 16
-p = 0

Contig extension inputs:
-o = 15
-m = 32
-r = 0.9


=>Mon Mar 7 15:40:17 2016: Reading, filtering and converting input sequences of library file initiated

------------------------------------------------------------

=>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

=>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

=>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
Thread 18 terminated abnormally: Can't open bwa output -- fatal
**************************************************

Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016

Please see the response of 'El Crazy Xabi' above.
Either use -x = 0 or use an older version of SSPACE.

[milo0615]

Could you present your whole command?

Hi sunnycqcn,

The command I used is as follows. Thank you for your help

>perl $HOME/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s gercombsadaptrim200_k44-contigs.fa -x 1 -z 200 -T 16 -k 3 -a 0.7 -m 32 -r 0.9 -p 0 -o 15 -n 10 -v 1 -b gercombsk44 &

[1] 20196

log:

[stilllab@b30-fac-staff-134-71-20-58 NEW_SSPACE_Gerreg]$ Your inserted inputs on [SSPACE_Standard_v3.0_linux] at Mon Mar 7 15:40:17 2016:
Required inputs:
-l = libraries.txt
Number of paired files = 2
-s = gercombsadaptrim200_k44-contigs.fa
-b = gercombsk44

Optional inputs:
-x = 1
-z = 200
-k = 3
-g = 0
-a = 0.7
-n = 10
-T = 16
-p = 0

Contig extension inputs:
-o = 15
-m = 32
-r = 0.9


=>Mon Mar 7 15:40:17 2016: Reading, filtering and converting input sequences of library file initiated

------------------------------------------------------------

=>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

=>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

=>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
Thread 18 terminated abnormally: Can't open bwa output -- fatal
**************************************************

Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016

[sunnycqcn]

Could you present your whole command?

Hello,

Were you guys able to figure it out? I am running SSPACE x_64 with options (x=1 and T=16) but I am getting the following error:

=>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

=>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

=>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
Thread 18 terminated abnormally: Can't open bwa output -- fatal
**************************************************

Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016


I would really appreciate your help.

[milo0615]

Hello,

Were you guys able to figure it out? I am running SSPACE x_64 with options (x=1 and T=16) but I am getting the following error:

=>Mon Mar 7 15:46:00 2016: Extending of contigs with unmapped reads

=>Mon Mar 7 15:46:00 2016: Building Bowtie index for contigs

=>Mon Mar 7 16:58:09 2016: Mapping reads to contigs with Bowtie
Thread 18 terminated abnormally: Can't open bwa output -- fatal
**************************************************

Process 'extend/format contigs' failed on Mon Mar 7 23:58:49 2016


I would really appreciate your help.

[El Crazy Xabi]

For those with the problem with the -x 1 "Process 'extend/format contigs' failed":
I wrote an email yesterday to the company that distributes the program (Baseclear) and they told me:

I understand this point, yet we do not have plans at this very moment to address this.
So please continue to use the –x 0 option. My apologies.

So I asked for a previous version and they send me the 2.0.

Good luck.

PS: the 2.0 needs Perl 4 ¬¬'

[sdsouza3]

Hi Boetsie,

I've used your program for an assembly that I'm working on and got some great results. I'm annotating the gaps in this assembly to prepare it for submission and I was curious--does SSPACE only report gaps with an estimated size or does it scaffold contigs with a placeholder gap of 100 N's? That is, do the N's between contigs represent gaps of known/estimated size or gaps of unknown size?

Thanks very much!

[sunnycqcn]

Did you solve your problem?

Greetings all! Another plea for wisdom from SSPACE users...

So, I am working on a 1.7Gb diploid de novo genome assembly (http://seqanswers.com/forums/showthread.php?t=42555) and wanted to try and employ some enhanced scaffolding to improve continuity of some of my existing draft assemblies. However, I get an error message upon completion of the sspace run:
"Process 'extend/format contigs' failed on Sat Dec 13 07:49:06 2014"

I have accepted default values to start with on the majority of the settings:
perl /home/jpummil/SSPACE-STANDARD-3.0_linux-x86_64/SSPACE_Standard_v3.0.pl -l libraries.txt -s Ray-53-contigs.fasta -x 1 -T 32 -b Ray_standard_out_v2_extend

Though sizeable (400GB memory and 18 hour runtime on 32 compute cores), not hitting any memory barriers, etc...job does complete and exit properly.

Think my libraries.txt is OK...
[jpummil@razor-l3 Snake_v2]$ more libraries.txt
lib1 bowtie /scratch/jpummil/Snake_v2/L001_R1_MiSeq.fastq /scratch/jpummil/Snake_v2/L001_R2_MiSeq.fastq 479 0.25 FR
lib2 bowtie /scratch/jpummil/Snake_v2/s1_R1_PE_Phred33.fastq /scratch/jpummil/Snake_v2/s1_R2_PE_Phred33.fastq 150 0.25 FR
lib3 bowtie /scratch/jpummil/Snake_v2/s2_R1_PE_Phred33.fastq /scratch/jpummil/Snake_v2/s2_R2_PE_Phred33.fastq 150 0.25 FR

Anything obvious come to mind? I had understood that with -x 1 flag, the assembly would be physically modified during the scaffolding process?

Thanks for any tips, and HAPPY HOLIDAYS!

______________________________________________
Did you solved your problem?
I met the same problem with you. If you have solved it, could you share it with me?
Thanks,
Fuyou