[AdrianP]

was the installation successful? Or did it give errors? Are you using perlbrew by any chance?

[ramesh.8v]

CPAN installation failed. I downloaded the module and installed using Makefile.PL. 'make test' was successful.

[AdrianP]

what about sudo make install?

[ramesh.8v]

Generating this error:
Catching error: "Can't write to '/home/ramesh/.cpan/sources/authors/id/Z/ZE/ZEFRAM/Perl4-CoreLibs-0.003.tar.gz.tmp13264-13264': Permission denied at /usr/local/share/perl/5.18.2/LWP/Protocol.pm line 105, <FIN> line 3. at /usr/local/share/perl/5.18.2/LWP/UserAgent.pm line 916, <FIN> line 3.\cJ" at /usr/local/share/perl/5.18.2/CPAN.pm line 392, <FIN> line 3.

[AdrianP]

looks like you need sudo rights, but it's odd that you need permission to write in your own home directory.

[ramesh.8v]

Finally! Upgrading perl and CPAN module helped me to solve the problem.

Thanks a ton!

[ramesh.8v]

Process 'extend/format contigs' failed on .....

Hi everyone,
As you guys previously discussed, I am getting following error,

Process 'extend/format contigs' failed on...

While using -x 1 option. -x 0 runs fine. If previous versions work fine, where do I get them?

I appreciate any kind of help.

Thanks

[ClemBuntu]

I think you can simply ask for it.
If not, send me a private message I should have sspace version 2 on my computer...

[marct]

Has there been any progress in the investigation into the issue with contig extension ( -x 1) using SSPACE version 3? I would like to try contig extension but am getting the same error as above:

Your inserted inputs on [SSPACE_Standard_v3.0_linux] at Tue Jun 2 19:53:34 2015:
Required inputs:
-l = Gag.library.file
Number of paired files = 4
-s = Gag_k83-contigs.fa
-b = Gag.SSPACE.1

Optional inputs:
-x = 1
-z = 200
-k = 5
-g = 0
-a = 0.5
-n = 15
-T = 24
-p = 1

Contig extension inputs:
-o = 15
-m = 85
-r = 0.9


=>Tue Jun 2 19:53:34 2015: Reading, filtering and converting input sequences of library file initiated

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

=>Tue Jun 2 20:37:23 2015: Extending of contigs with unmapped reads

=>Tue Jun 2 20:37:23 2015: Building Bowtie index for contigs

=>Wed Jun 3 00:40:25 2015: Mapping reads to contigs with Bowtie
Thread 31 terminated abnormally: Can't open bwa output -- fatal
Thread 32 terminated abnormally: Can't open bwa output -- fatal
Thread 33 terminated abnormally: Can't open bwa output -- fatal
Thread 34 terminated abnormally: Can't open bwa output -- fatal
Thread 35 terminated abnormally: Can't open bwa output -- fatal
Thread 36 terminated abnormally: Can't open bwa output -- fatal
Thread 37 terminated abnormally: Can't open bwa output -- fatal

[illinu]

I was running the SSPACE-STANDARD-3.0_linux-x86_64 in my computer and was getting that error, then I changed to the cloud and could chose another perl version (I was getting some perl errors, like this perl was not built to support threads or something like that), I don't remember which one worked for me, either 18 or 20 but I think I also needed to turn the -x flag from 1 to 0 and then it worked!!

[Zhangxj]

i got the same error, using -x 1 to extend the contigs, and faild when use the v3.0 version

=>Sat Jul 18 11:34:06 2015: Mapping reads to contigs with BWA
**************************************************

Process 'extend/format contigs' failed on Sun Jul 19 00:28:39 2015

[rittza]

Same problem here...
I came across this while testing SSPACE with the provided tutorial, before trying my own data.

it runs smoothly if no extension is used, but using -x 1, I get:

=>Wed Aug 26 17:19:16 2015: Mapping reads to contigs with Bowtie
Thread 4 terminated abnormally: Can't open bwa output -- fatal
Thread 5 terminated abnormally: Can't open bwa output -- fatal
etc...

Silly question probably, but anyone know why is it that when the read aligner designated in the library file is bowtie, BWA is still mentioned during processing?

The processing seems to have had some errors, so now I'm not sure of what to do of the output...is it complete or not really?

Thanks in advance

[sunnycqcn]

i got the same error, using -x 1 to extend the contigs, and faild when use the v3.0 version

=>Sat Jul 18 11:34:06 2015: Mapping reads to contigs with BWA
**************************************************

Process 'extend/format contigs' failed on Sun Jul 19 00:28:39 2015

———————————————————————————————————————
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

[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

[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!