Question: (Closed) abyss-pe command line options
1
gravatar for Mbillah
10 months ago by
Mbillah110
Chittagong
Mbillah110 wrote:

I have some reads, I want to assembly this read by abyss. I've got some commands, it's one of them. I do not understand the end of it. The command is
abyss-pe in="../CS3270_A8733_GCCAAT_L001_R1.fastq ../CS3270_A8733_GCCAAT_L001_R2.fastq" k=71 name=CS3270_abyss_k71 np=4 > CS3270_abyss_k71.log 2>&1 what does it mean CS3270_abyss_k71.log 2>&1 ? TIA

abyss assembly • 543 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by Mbillah110

Hello Mbillah!

Given your history of poorly formatted and low-effort questions, I will close this post until you properly format it and elaborate on the problem.

Also, 2>&1 can be easily googled.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 10 months ago • written 10 months ago by ATpoint22k
1

I know that abyss-pe name=test k=96 in='reads1.fa reads2.fa' this command produce all output. so abyss-pe name=test k=96 in='reads1.fa reads2.fa' > test.log. test.log file contain which information?

ADD REPLYlink written 10 months ago by Mbillah110
1

I will quickly and briefly answer (just because I'm an abyss fan) but ATpoint remarks are still valid, do try to put some effort in this!

test.log file contain which information?

that will contain the runtime information, that is the info that would normally be printed to screen (such as 'reading file X', some intermediate stats or such) , nothing essential in there but it might help to diagnose if there are issues .

ADD REPLYlink modified 10 months ago • written 10 months ago by lieven.sterck5.8k
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@lieven.sterck thank you for your kind reply.

ADD REPLYlink written 10 months ago by Mbillah110
1

I need your help, I tried to get 140 million read assembly, But memory could not load it(sparsehash fatal error). As a result I divided my fastq file and created two contig file (70 million reads). is there any quality problem? and now I want to make this contig file one. how can I do this?

ADD REPLYlink modified 10 months ago • written 10 months ago by Mbillah110
3

Hi Mbillah ,

please do read the posts above again. ATpoint already closed it (I did you a favor there already) and this looks like a new question, so best open a new post then ( and take ATpoint comments into consideration ;) )

btw, you already have a thread ABySS path setup for temporary files on this topic, why don't you continue that one?

ADD REPLYlink modified 10 months ago • written 10 months ago by lieven.sterck5.8k
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