Re: [Samtools-help] samtools truncated file and Exec format error

[John M. <Joh...@gl...>]

On 8 Nov 2017, at 11:36, Tommy Carstensen <tc...@sa...<mailto:tc...@sa...>> wrote:
2) Furthermore, when typing the command below:
samtools view -H ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram

Then I get this error:
samtools view: failed to open "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram" for reading: Exec format error

"Exec format error" here means that samtools/HTSlib's format detection code was unable to determine what format this file was (which it tries to do by examining its first few tens or hundreds of bytes).

Sure enough, if you download that one, I think you'll find its first 100Mb or so are all zeros...

    John