using my own mate pair histogram for scaffolding

[Julie Hussin]

Hi,

I have been running abyss to the contigs stage, and I would like to run the scaffolding step, but with my own pre-computed mate pair histogram.

What's the best way to do this?

I thought I could first run abyss-pe with "contigs contigs-dot" and then just change the command line (by removing contigs contigs-dot) to restart the assembly at the scaffolding step, having put the .hist file in the directory, however, performing a dry-run outputs all the command lines, starting back from ABYSS-P step. 

I can comment out the unwanted lines, however I am worried that the first command below will overwrite my pre-computed histogram (index05-6.hist), but I probably need index05-6.dist.dot to be computed before launching abyss-scaffold, right?

abyss-map  -j5 -l72    /well/donnelly/PlatypusSeq/julie/MATEPAIR_BAMS/index05_stampy_dedup.sorted.bam /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res72_3_20_100/FULL3MALES_72-6.fa \

                |abyss-fixmate  -l72  -h index05-6.hist \

                |sort -snk3 -k4 \

                |DistanceEst --dot  -j5 -k72 -l72 -s100 -n3   -o index05-6.dist.dot index05-6.hist

abyss-scaffold   -k72 -s100 -n3 -g /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res72_3_20_100/FULL3MALES_72-6.path.dot  /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res72_3_20_100/FULL3MALES_72-6.dot index05-6.dist.dot >/well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res72_3_20_100/FULL3MALES_72-6.path

Many thanks and best wishes,

Julie

[Ben Vandervalk]

 Hi Julie,

Yes, it is possible to resume the assembly, and you've got the right idea by testing with --dry-run option.  It just takes a bit of fiddling.

Try specifying 'scaffolds' explicitly as your target and/or using the make '-o' option to specify files you *don't* want to rebuild.

e.g.

$ abyss-pe <...your abyss-pe options> --dry-run -o index05-6.dist.dot scaffolds

- Ben

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[Julie Hussin]

Hi Ben,

thank you for your quick response.

I tried what you suggested, and succeeded in getting the commands to do the scaffolding only (checking with --dry-run), however, the index05-6.hist file I created was overwritten despite the fact that I use the -o option.

Here's my command line :

abyss-pe np=6 k=72 name=/well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res72_3_20_100/FULL3MALES_72 lib='lib1 lib2 lib3' mp='index05' lib1='/well/donnelly/PlatypusSeq/julie/SHORTREADS_BAMS/N701_nodups.bam' lib2='/well/donnelly/PlatypusSeq/julie/SHORTREADS_BAMS/N702_nodups.bam' lib3='/well/donnelly/PlatypusSeq/julie/SHORTREADS_BAMS/N705_nodups.bam' index05='/well/donnelly/PlatypusSeq/julie/MATEPAIR_BAMS/index05_stampy_dedup.sorted.bam' n=3 m=20 s=100 -o index05-6.hist scaffolds

Here are the commands launched (according to dry-run):

abyss-map  -j6 -l75    /well/donnelly/PlatypusSeq/julie/MATEPAIR_BAMS/index05_stampy_dedup.sorted.bam /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.fa \

                |abyss-fixmate  -l75  -h index05-6.hist \

                |sort -snk3 -k4 \

                |DistanceEst --dot  -j6 -k75 -l75 -s100 -n3   -o index05-6.dist.dot index05-6.hist

abyss-scaffold   -k75 -s100 -n3 -g /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.path.dot  /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.dot index05-6.dist.dot >/well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.path

PathConsensus  -k75 -p0.9 -s /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-7.fa -g /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-7.adj -o /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-7.path /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.fa /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.dot /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.path

cat /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-6.fa /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-7.fa \

                |MergeContigs  -k75 -o /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-8.fa - /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-7.adj /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-7.path

ln -sf /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-8.fa /well/donnelly/julieh/ABYSS/PLATYPUS/FULL3MALES/res75_3_20_100/FULL3MALES_75-scaffolds.fa

What I would like is to use my custom made index05-6.hist, but although it was in the directory, it was re-created after the first command.

Many thanks

Julie

[Ben Vandervalk]

Hi Julie,

Oh, I see what the problem is now:  index05-6.hist and index05-6.dist.dot are being created in the same command-line pipe, and the creation of index05-6.dist.dot depends on index05-6.hist.

Here is a workaround that will hopefully do what you need:

Step 1:

$ abyss-pe <your abyss-pe params> pe-sam

Step 2:

Overwrite the generated hist file with your own.

Step 3:

$ abyss-pe <your abyss-pe params> scaffolds

Keep using the --dry-run option at each step to make sure things are going as expected!

- Ben

[Ben Vandervalk]

Hi Julie,

Sorry, I meant to say "mp-sam" (not "pe-sam") for Step 1.

- Ben

[Julie Hussin]

Hi Ben!

Yes, I figured it was mp-sam!

And it works :)

Many thanks for your help,

Julie

[Ben Vandervalk]

Glad to hear!  (Thanks for letting me know.)

- Ben