Trouble running sealer, looking for test/example data?

[Scott Geib]

Hi, 
I am running Abyss-sealer, and was getting basically empty outputs.  the X_log.txt , X_merged.fa and X_scaffold.fa are written but are empty, I get nothing written to std err or out.  I wanted to try it out with test data to make sure my installation is sound (this was a fresh install to V1.9 to utilize sealer).  Is there test data located anywhere in the distribution on github?  If not, anyone have similar issues or thoughts?  My command is as follows (a very simple command just to ensure things are functioning):

abyss-sealer -k90 -o test -S genome.fa reads.fq

Reads are a fastq file of 100 bp shotgun reads (the first read of a paired end run, just using for testing, ~60X coverage of genome). 

ultimately would run something like this if I can get things working:

abyss-sealer -k90 -k80 -k70 -k60 -k50 -k40 -k30 -o $OUT -S $GENOME -P 10 -j $CPU -e $READS1 $READS2

Thanks

Scott

[Ben Vandervalk]

Hi Scott,

That is very strange.   Can you post your full log output from Sealer? (or send it in a private e-mail if you prefer).

Unfortunately, there is no test data set that comes with Sealer.  It definitely would be nicer if our tools came with test data sets (or at least scripts to download test data).

- Ben

--
You received this message because you are subscribed to the Google Groups "ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to abyss-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Jennifer Shelton]

Are your sure your job completed? Output is written to those files only when a run is complete. I am also running sealer and I use the freely available datasets from the sealer paper to test runs. You might try the small E. coli dataset. 

You can download these files with sratoolkit: 

cd /home/me/out/

nohup fastq-dump --split-files -A SRR959238 &> log.txt

then do a n Abyss assembly for your draft genome fasta:

abyss-pe k=50 name=e_coli -j 8 -C ~/out/e_coli_assembly_qsub in='/home/me/out/SRR959238_1.fastq /home/me/out/SRR959238_2.fastq'