Empty output sealer-abyss

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Melissa hpy

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Oct 5, 2021, 6:02:49 PM10/5/21
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Hi, 

I´m running sealer-abyss but I´m getting empty outputs. Since the command starts to run, test_log.txt , test_merged.fa, and test_scaffold.fa are created but after one day of running these files are still empty, and the std err out file is empty too.  The barcodes that I´m using are linked reads that were treated using the long-ranger basic command. This is the command that I´m using:

module load abyss/2.3.1

abyss-sealer -b20G -k64 -k80 -k96 -k112 -k128 -o test -S draft_arcs.fa reads1.fq.gz

I don´t know if I´m doing something wrong

Thank you in advance for your help

Melissa 

Lauren Coombe

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Oct 5, 2021, 6:09:24 PM10/5/21
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Hi Melissa,

A couple of things - do you see your process still running (ex. with `top`?) With a 20G Bloom filter, I'd also suggest running with multiple threads - so using -j. Also, you can use -v to have verbose output. 
If you re-run with those conditions, and see that the process is still doing nothing, I would suggest running a smaller test with a couple of scaffolds and some reads. That way, you can ensure that your installation is working correctly.

Thanks for your interest in ABySS!
Lauren

Melissa hpy

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Oct 7, 2021, 7:18:39 PM10/7/21
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Hi Lauren,

This morning (6h ago) I ran the command again and the outputs are still empty, but the stdr file says this:

Finding flanks
124083 gaps found
124006 flanks extracted

Building bloom filter

Is this normal?

Thank you,

Melissa

Lauren Coombe

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Oct 7, 2021, 7:21:28 PM10/7/21
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Hi Melissa,

That indicates that the program is still adding your input reads to the Bloom filter data structure. So, how long that takes really varies widely depending on how many threads you specified, and how many reads are in your input file. If you want a sense of how far through the file the program is, I like using the unix command "pv -pd <pid>", where you can just find the process ID of sealer using 'top'.
If you want it to go faster, increasing the threads will help with that.

Lauren

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