User: Toto26

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Toto2610
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1 month, 2 weeks ago
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6 months, 2 weeks ago
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b****************@gmail.com

Posts by Toto26

<prev • 83 results • page 1 of 9 • next >
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Comment: C: Issue using IDBA
... OK sorry for that, here are the file contents of .error and .out: more ACG-006_assembly.error /var/spool/torque/mom_priv/jobs/15583407.SC: line 28: 30378 Killed $IDBA'bi n/idba_ud' --pre_correction -o /pandata/LEPIWASP/ACG-0006_0027/OUT-0006-2 -r $INPUT1'.fa' --num_thr ...
written 7 weeks ago by Toto2610
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Comment: C: De novo assembly programm
... Megahit is running but does it give me a scaffold.fa output? I only can see contig output file ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... OK, so I should use MEGAHit instead of Spades for my data? It also can take only paired-end right? In fact I'm looking for anassembler tools which is not complicate to use and can accept only paired-end for a large genome. Is planatus the easiest to handle? ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... Hi chris, Spades is actually running, maybe it will work? If Spades does no work I'll try Plantanus as you advise me but if Spades is running it does mean that it is ok for my data is not it? Note that I do not really need a perfect assembled genome, for exemple I used IDBA_ud for the genome of an ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... Yes so if the job is killed I guess that I cannot continue at the checkpoint. I put it on a 1 week queue it's ok. ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... Ok thank you because when I put it on a 1day queue I get a broken pipe in the .error file; do you know how can I continue at the checkpoint when I run another time in a queue 1 day instead of restarting from zero? ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... I'm not aware of that but I know that it is a butterfly genome full by repeat elements. ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... Thank you very much !! it's running and I used: #PBS -S /bin/bash #PBS -l nodes=1:ppn=8:bigmem,mem=100gb #PBS -e /pandata/LEPIWASP/ACG-0006_0027/0006-spades.error #PBS -o /pandata/LEPIWASP/ACG-0006_0027/0006-spades.out #PBS -N ACG-0006_spades #PBS -q q1hour il ...
written 3 months ago by Toto2610
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Comment: C: Makefile:65: recipe for target 'SOAPdenovo-63mer' failed
... In fact it is in my lab server, how can I know the version you are asking for, I'm not admin. ...
written 3 months ago by Toto2610
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Comment: C: De novo assembly programm
... Thank you, for your help to all, I will try the soap after making Kmer estimation. I'll let you know how it goes. I'm on a lab server, I think it should be ok for the RAM. @h.mon I already done an assembly for another sample for the same specie and I got a coverage about 10X and I checked the qua ...
written 3 months ago by Toto2610

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Popular Question 3 months ago, created a question with more than 1,000 views. For compare 2 dataframe with pandas
Popular Question 3 months ago, created a question with more than 1,000 views. For C extension: No module named 'pandas._libs.tslib' not built (pandas)
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