Question: abyss fixmate error
0
gravatar for rebzi87
4.2 years ago by
rebzi870
United States
rebzi870 wrote:

Hi -

I'm trying to do a de novo assembly using Illumina paired-end reads and 3 mate-pair libraries of different insert length. I use the command:

> abyss-pe np=32 k=61 name=wagtail lib='pe1' mp='mp1 mp2 mp3 mp4 mp5 mp6 mp7 mp8 mp9' \
pe1='cutadapt1.fq.gz cutadapt2.fq.gz' mp1='2kb-out_A_R1.fasta.gz 2kb-out_A_R2.fasta.gz' \
mp2='2kb-out_B_R1.fasta.gz 2kb-out_B_R2.fasta.gz' mp3='2kb-out_C_R1.fasta.gz 2kb-out_C_R2.fasta.gz' \
mp4='4kb-out_A_R1.fasta.gz 4kb-out_A_R2.fasta.gz' mp5='4kb-out_B_R1.fasta.gz 4kb-out_B_R2.fasta.gz' \
mp6='4kb-out_C_R1.fasta.gz 4kb-out_C_R2.fasta.gz' mp7='9kb-RCout_A_R1.fasta.gz 9kb-RCout_A_R2.fasta.gz' \
mp8='9kb-RCout_B_R1.fasta.gz 9kb-RCout_B_R2.fasta.gz' mp9='9kb-RCout_C_R1.fasta.gz 9kb-RCout_C_R2.fasta.gz'

where each mate-pair library has group A, B, and C as output by the quality filtering program NextTrim. I keep getting the following error:Building the suffix array...
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Mateless   0
Unaligned  0
Singleton  0
FR         0
RF         0
FF         0
Different  0
Total      0
abyss-fixmate: error: All reads are mateless. This can happen when first and second read IDs do not match.
error: `pe1-3.hist': No such file or directory
make: *** [pe1-3.dist] Error 1
make: *** Deleting file `pe1-3.dist'

 

I saw a past post about the naming of paired reads and changed the files to have the /1 /2 naming format (instead of a space) so I changed my fasta file names from: 

>D00723:25:C6C71ANXX:4:1101:1748:2147 1:N:0:14

>D00723:25:C6C71ANXX:4:1101:1748:2147/1

I still get the same errors and am at a loss of what to do. Any help would be greatly appreciated! Thanks.

 

 

 

 

abyss • 1.7k views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 4.2 years ago by rebzi870

It may be because your left and right reads are very different sizes. I got the same error after Trimmomatic discarded most of my left reads.

ADD REPLYlink written 3.6 years ago by san.san90
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