abyss-pe command line options
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
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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>&1can 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!
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?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!
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 .
@lieven.sterck thank you for your kind reply.
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?
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?