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WeichenZhou / PALMER

Pre-mAsking Long reads for Mobile Element inseRtion
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BLAST engine error: Warning: Sequence contains no data #14

Closed Soniazumalave closed 4 years ago

Soniazumalave commented 4 years ago

I am getting these warnings when running PALMER:

BLAST engine error: Warning: Sequence contains no data BLAST engine error: Warning: Sequence contains no data BLAST engine error: Warning: Sequence contains no data BLAST engine error: Warning: Sequence contains no data Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 69 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 63 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 73 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 61 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 61 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 63 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 73 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 72 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 72 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 56 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 69 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 72 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 72 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 62 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 72 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 74 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 70 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 69 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 72 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 61 Warning: (1431.1) CFastaReader: Ignoring invalid residue at line 2, position 57

The command I use is: ./PALMER --input $sampleBam --workdir $wkDir/ --ref_ver hg19 --output NA12878 --type LINE --chr 21 --ref_fa $refFasta

And the PALMER version is 1.4.

I've read it is related to the presence of ambiguous nucleotides (N's) in the reference genome. Which reference do you use? Is it masked? Would these warnings affect the results?

The head of my reference looks like this:

1 dna:chromosome chromosome:GRCh37:1:1:249250621:1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Thank you in advance!

WeichenZhou commented 4 years ago

Hi Sonia,

Thanks for using PALMER. The head of the reference should be as what you saw. And your command line looks good too. The error information from BLAST sometime happens, because of the string of 'N'. Yet, it should not affect your final results.

Let me know if you have any further questions! Cheers