Hi guys,
I really don't understand, always got a problem to make an abyss with real data :(
Got this in my log (full log here: )
abyss-map: missing arguments
abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match.
error: `../FQ_file/Cfinal_bwa_refXRQ_SF099_primALN_mapped_PE.fq-3.hist': No such file or directory
make: *** [../FQ_file/Cfinal_bwa_refXRQ_SF099_primALN_mapped_PE.fq-3.dist] Erreur 1
make: *** Destruction du fichier « ../FQ_file/Cfinal_bwa_refXRQ_SF099_primALN_mapped_PE.fq-3.dist »
I got this version of Abyss: 1.5.2 and launch this command:
abyss-pe contigs mp="" clean name=mappedR_SEPE k=60 j=25 s=250 in='PE.fq' pe='PE.fq' se='SE.fq'
Actually in my PE.fq file there is /1 and /2 paires, but sometimes two /1 can be retrieved, and then got an interleaved file. But in manuals, it says it can work even with that format.
example (PE.fq):
advance thanks
Hi Siva,
Try this instead:
$ abyss-pe contigs clean name=mappedR_SEPE k=60 j=25 s=250 in='PE.fq'
The fact that you have duplicate reads with the "/1" suffix in your file indicates that there is a serious problem with your data. In order to get a good assembly, you will probably need to solve that problem.
Hi Benv, I'll not try with PE only because I wanted to make contigs with single end reads also.
Then yea I also think that problem is coming from my files, I got it from a "bwa mem" mapping and so have none unique alignment that's why having multiple /1 or multiple /2.
But I've made a filtering before with -F 256 with samtools, so don"t understand why there is yet not primary alignment.
I'll check...
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I got these files, but not final contig file: