Download genome files not working?

[RonKeller]

dear community,

I attempted to download all available E coli genomes from the NCBI database using your package via this command:
ncbi-genome-download --species-taxids 562 bacteria

This finished without any problems, and yielded about 38 000 output folders in the subfolders refseq/bacteria/ .
However, when I checked those, most contained exactly one file
MD5SUMS
which looks like this:
201a7cdb8790811d81e20272b4f0dc0b ./annotation_hashes.txt e02ba9d6e803764a0f2fb6426f235dbd ./GCF_017117745.1_ASM1711774v1_assembly_report.txt 3cb5e81c0fc96aa50d9e402cfedc68e9 ./GCF_017117745.1_ASM1711774v1_assembly_stats.txt 58a500b8e6d12ba89d7258c56eea3646 ./GCF_017117745.1_ASM1711774v1_cds_from_genomic.fna.gz 3d0342f149e9e799b6bb11aa67606af7 ./GCF_017117745.1_ASM1711774v1_feature_count.txt 0537f0fddec806fffe92683f2b50c8f0 ./GCF_017117745.1_ASM1711774v1_feature_table.txt.gz 614fa5a918f91e9d0348a4f3f646a647 ./GCF_017117745.1_ASM1711774v1_genomic.fna.gz 9a9f2f71a0ae8dc0355306aeef48d239 ./GCF_017117745.1_ASM1711774v1_genomic.gbff.gz 620f9ff372b7bd0a3514a04623ec967a ./GCF_017117745.1_ASM1711774v1_genomic.gff.gz 5d1c171dcd2c8814180ef06da3273b1b ./GCF_017117745.1_ASM1711774v1_genomic.gtf.gz be0ba445b06b2ab2dfc183370a1f63fc ./GCF_017117745.1_ASM1711774v1_protein.faa.gz 76a67055c935f89f231b449cf86fcb28 ./GCF_017117745.1_ASM1711774v1_protein.gpff.gz ac3253b88edb24e979dd53706876517d ./GCF_017117745.1_ASM1711774v1_rna_from_genomic.fna.gz cbe26f962ecd9f7e6d1e0ed3afd369b3 ./GCF_017117745.1_ASM1711774v1_translated_cds.faa.gz bb14c6511a80dbc60878b22521cb3a17 ./GCF_017117745.1_ASM1711774v1_wgsmaster.gbff.gz
However, I cannot find the files mentioned here on my drive; if I check the folder contents, only 79 of the 38 000 folders contain more than one file, and that file is MD5SUMS.

What am I missing here? Those files should be in the same folder as the MD5 file, right?

Best
Ronald

[kblin]

Are you sure the command finished successfully? Because ncbi-genome-download will get the md5sum files first, and then download the sequence files. You could try running the command again, maybe with --progress-bar if you're running interactively.