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  • uloeber
    replied
    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

    Leave a comment:


  • darthsequencer
    replied
    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?

    Leave a comment:


  • sunnycqcn
    replied
    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.




    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

    Leave a comment:


  • sunnycqcn
    replied
    How many libraries is in your libraries files.


    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

    Leave a comment:


  • milo0615
    replied
    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

    Leave a comment:


  • El Crazy Xabi
    replied
    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

    Leave a comment:


  • sunnycqcn
    replied
    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.



    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

    Leave a comment:


  • milo0615
    replied
    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

    Leave a comment:


  • fahmida
    replied
    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.

    Leave a comment:


  • milo0615
    replied
    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

    Leave a comment:


  • sunnycqcn
    replied
    Could you present your whole command?




    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.

    Leave a comment:


  • milo0615
    replied
    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.

    Leave a comment:


  • El Crazy Xabi
    replied
    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 ¬¬'
    Last edited by El Crazy Xabi; 02-09-2016, 04:12 PM.

    Leave a comment:


  • sdsouza3
    replied
    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!

    Leave a comment:


  • sunnycqcn
    replied
    Did you solve your problem?

    Originally posted by jpummil View Post
    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

    Leave a comment:

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