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Old 02-09-2016, 03:03 PM   #241
El Crazy Xabi
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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:
Quote:
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 '

Last edited by El Crazy Xabi; 02-09-2016 at 03:12 PM.
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Old 03-08-2016, 10:53 AM   #242
milo0615
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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.
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Old 03-08-2016, 12:16 PM   #243
sunnycqcn
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Could you present your whole command?




Quote:
Originally Posted by milo0615 View Post
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.
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Old 03-08-2016, 12:52 PM   #244
milo0615
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Quote:
Originally Posted by sunnycqcn View Post
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
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Old 03-08-2016, 01:10 PM   #245
fahmida
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Quote:
Originally Posted by milo0615 View Post
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.
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Old 03-08-2016, 02:07 PM   #246
milo0615
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Quote:
Originally Posted by fahmida View Post
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
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Old 03-08-2016, 02:58 PM   #247
sunnycqcn
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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.



Quote:
Originally Posted by milo0615 View Post
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
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Old 03-08-2016, 03:03 PM   #248
El Crazy Xabi
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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
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Old 03-08-2016, 03:10 PM   #249
milo0615
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Quote:
Originally Posted by sunnycqcn View Post
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
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Old 03-08-2016, 03:24 PM   #250
sunnycqcn
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How many libraries is in your libraries files.


Quote:
Originally Posted by milo0615 View Post
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
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Old 03-08-2016, 03:29 PM   #251
sunnycqcn
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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.




Quote:
Originally Posted by milo0615 View Post
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
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Old 06-01-2016, 07:46 AM   #252
darthsequencer
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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?
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Old 03-07-2019, 03:19 AM   #253
uloeber
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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
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