Read file exception when use platunas to assemble plant genome

Question

[tigerhui587]

Hi,

I used my normalized fastq files to assemble, but it always said 'Read file exception!!'

Below is my script and the error. How to fix it? Thanks a lot!

/path/to/platanus assemble \
  -k 21 \
  -u 1.0 \
  -f /path/to/DNA-1_CGATGT_L002_R1_001_paired_trimmed_paired_1.fastq.normalized_K25_C30_pctSD200.fq \
     /path/to/DNA-1_CGATGT_L002_R1_001_paired_trimmed_paired_2.fastq.normalized_K25_C30_pctSD200.fq \
     /path/to/SM01-PBU1_GTCCGC_L005_R1_001_paired_trimmed_paired_1.fastq.normalized_K25_C30_pctSD200.fq \
     /path/to/SM01-PBU1_GTCCGC_L005_R1_001_paired_trimmed_paired_2.fastq.normalized_K25_C30_pctSD200.fq \
     /path/to/SM01-PBU1-7k_CCGTCC_L005_R1_001_paired_trimmed_paired_1.fastq.normalized_K25_C30_pctSD200.fq \
     /path/to/SM01-PBU1-7k_CCGTCC_L005_R1_001_paired_trimmed_paired_2.fastq.normalized_K25_C30_pctSD200.fq \
  -o /diag/home/hzz0036/goosegrass_genome/platanus

Error(2): Read file exception!!
Read file exception!!
Read file is not FASTA/FASTQ format.

Hui

[Nicola Casiraghi]

It seems that your normalized input fastq files are not correctly formatted. Does the command work if you pass not-normalized fastq files? Try to check if there are differences between your not-normalized and normalized fastq files.

[tigerhui587]

Hi Nicola,

I tried to use not-normalized fastq files, but it also said read file exception. It seems the platunas software problem.

Hui

[haombio]

Hi Hui

I came across these problems,too. Therefore I wonder if you have solved the errors yet.