error in extracting one chromosome from multiple fasta files to a single fasta file


Hello All,

I have multiple fasta files. I want to make output files for each chromosome from all the fasta files. For example, output file all_ch1.fasta will have ch1 sequences from all the fasta files and so on. I tried:

samtools faidx *fasta.gz ch1 > all_ch1.fasta

But I am getting this error:

[W::fai_get_val] Reference sample2.fasta.gz not found in FASTA file, returning empty sequence
[faidx] Failed to fetch sequence in sample2.fasta.gz

I checked sample2.fasta.gz file but it is not empty. Thank you for any help!



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