Lastl error (bad FASTQ data: missing '@)

[pinnintil...@gmail.com]

Hi,

I trying to align human genome datasets against hg38.fa. I'm able to build the db for hg38. While alignment, I'm facing the same error with i supply some parameters to command line. Is any thing wrong with the CMD

First - no parameters provided able to generate a maf file.

 ./lastal  hg38  /data/Likith/Ref/hg38.fa /data/Likith/benchmarkdatasets/Chi-son/sickle_SRR2962693_R1q20.fastq   /data/Likith/benchmarkdatasets/Chi-son/sickle_SRR2962693_R2q20.fastq > out3.maf

Second - with parameters showed an error( bad FASTQ data: missing '@)

./lastal -Q3 -P20 -e120 hg38 /data/Likith/Ref/hg38.fa /data/Likith/benchmarkdatasets/Chi-son/sickle_SRR2962693_R1q20.fastq /data/Likith/benchmarkdatasets/Chi-son/sickle_SRR2962693_R2q20.fastq > out3.maf
./lastal: bad FASTQ data: missing '@'

I'm not able to figure it out. Any anything wrong with my command.

thanks for your comments

[Frith, Martin]

Hi there

the main thing is to omit "/data/Likith/Ref/hg38.fa" from the lastal commands.

Have a nice day,

Martin

https://sites.google.com/site/mcfrith/

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