Denovo assembly using Abyss-pe

Question

[sunnykevin97]

HI

Trying to perform denovo assembly using Abyss shows error.

I tried to run all the 10 samples, same error all the time.

Suggestion please.

abyss-pe name=A_ven k=21 in='A_ventrim.R1.fastq A_ventrim.R2.fastq' 

error: sequence with ID `NB501461:181:HLVK3BGXL:1:11101:19919:1765/1' is empty

 head *R1.fastq

@NB501461:181:HLVK3BGXL:1:11101:7033:1042 1:N:0:GTCAGT
TCGTCNACCTCTGCTCAGCGGCGGCGGCGGGGGGCCGCGGCGGGGGCTTATGTCGTCGTAGTCCCTCCTGGAGGGAGGCATGGGTCGGTTCCCGCGAACAGGGGGCATGCGCTCGAAGCCGCCGCGCACGCGAATGGGGAAGCCGCCGATG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEE/EEEEEEEEEAEAEEEEEEEEEEEEEEEEEEE<EEA
@NB501461:181:HLVK3BGXL:1:11101:10369:1042 1:N:0:GTCAGT
TCTTTNTTTTAATAACTGTAGGATACATCAGCACTTCCCCGTTATACTTCACTTTAAACTCTAAGGCTGTGTGTGTGTGTGTGTGTGTGTGTGTTTAGGCAAACTGCGTAGGTGTGTATAATTATATTACTCAGAGAAGAGAAGTGCTGGA
+
AAAAA#EEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEE6EEEEEEE<EEEEEEEEEEAE/AEEEE/EEEE<AEA/A/EEEA/EEEEEEEE/
@NB501461:181:HLVK3BGXL:1:11101:20005:1043 1:N:0:GTCAGT
AGCCANATTAAAGCAGTCATTTCCTTCCAGGTGATTTGAAGTCAAAATAATAACTGAGTGTTTCTAGGAAAATCTGAGTCAGCGGTTAACAACAATGAGTGATCGAGTGGATCCACAGCACCAGCAGCTGACTGTGTATTTTATATTTAAC

Answer 1

[Mensur Dlakic]

error: sequence with ID `NB501461:181:HLVK3BGXL:1:11101:19919:1765/1' is empty

I can't imagine any clearer error message than this. It tells you that a left read (in R1) with that particular ID number is empty.

Below are several links to posts about removing empty reads.

• remove empty reads from fastq files
• How to remove empty read from fastq

[GenoMax]

Unless OP has a mix of files with different headers.

Error refers to /1 in headers yet the example posted above has more current 1:N:0:GTCAGT headers.