I am trying to donwload the microbial genome using the repophlan_get_microbes.py (https://github.com/SegataLab/repophlan) but now it is running more than 10 days and still not finished on slurm HPC.
Could anyone please suggest what is the issue with the script?
#!/bin/bash
#SBATCH --job-name=download.GENOME # Job name
#SBATCH --ntasks=60
#SBATCH --nodes=3 # Number of nodes
#SBATCH --time=2000:00:00 # Time limit hrs:min:sec
#SBATCH --partition=k2-himem
#SBATCH --mem=800G
module add apps/python3/3.7.4/gcc-4.8.5
module add libs/biopython/1.73/gcc-4.8.5+python-2.7.8+numpy-1.16.0
python repophlan_get_microbes.py --taxonomy taxonomy_reduced.txt --out_dir microbes --nproc 20 --out_summary repophlan_microbes.txt | tee repophlan_microbes.log
$ head repophlan_microbes.log
2020-09-17 20:44:59,964 ./repophlan_get_microbes.py INFO Reading the taxonomy from taxonomy_reduced.txt...
2020-09-17 20:45:04,921 ./repophlan_get_microbes.py INFO Done.
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000001215.4 [Drosophila melanogaster ] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000001405.39 [Homo sapiens ] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000001635.26 [Mus musculus ] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000001735.4 [Arabidopsis thaliana ecotype=Columbia] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000001895.5 [Rattus norvegicus strain=mixed] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000001905.1 [Loxodonta africana ] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000002035.6 [Danio rerio ] excluded from download because of uninteresting phyla!
2020-09-17 20:45:10,716 ./repophlan_get_microbes.py WARNING GCF_000002075.1 [Aplysia californica ] excluded from download because of uninteresting phyla!
$ tail repophlan_microbes.log
2020-09-21 20:42:26,871 repophlan_get_microbes.py INFO Parsing of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/635/075/GCA_001635075.1_ASM163507v1/GCA_001635075.1_ASM163507v1_genomic.gbff.gz
2020-09-21 20:42:27,198 repophlan_get_microbes.py INFO Parsing of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/319/175/GCA_010319175.1_PDT000567389.1/GCA_010319175.1_PDT000567389.1_genomic.gbff.gz
2020-09-21 20:42:27,482 repophlan_get_microbes.py INFO Parsing of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/518/025/GCA_003518025.1_ASM351802v1/GCA_003518025.1_ASM351802v1_protein.faa.gz
2020-09-21 20:42:27,608 repophlan_get_microbes.py INFO Parsing of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/788/535/GCA_001788535.1_ASM178853v1/GCA_001788535.1_ASM178853v1_protein.faa.gz
2020-09-21 20:42:27,628 repophlan_get_microbes.py WARNING No remote file found (some ffn and faa are know to be missing remotely). Aborting the download of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/997/445/GCA_010997445.1_ASM1099744v1/GCA_010997445.1_ASM1099744v1_protein.faa.gz. <urlopen error ftp error: [Errno ftp error] 550 GCA_010997445.1_ASM1099744v1_protein.faa.gz: No such file or directory>
2020-09-21 20:42:27,628 repophlan_get_microbes.py ERROR Error in downloading of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/997/445/GCA_010997445.1_ASM1099744v1/GCA_010997445.1_ASM1099744v1_protein.faa.gz <urlopen error ftp error: [Errno ftp error] 550 GCA_010997445.1_ASM1099744v1_protein.faa.gz: No such file or directory>
2020-09-21 20:42:27,628 repophlan_get_microbes.py ERROR Error in downloading of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/997/445/GCA_010997445.1_ASM1099744v1/GCA_010997445.1_ASM1099744v1_protein.faa.gz: empty fna file!
2020-09-21 20:42:28,239 repophlan_get_microbes.py WARNING No remote file found (some ffn and faa are know to be missing remotely). Aborting the download of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/778/895/GCA_902778895.1_Rumen_uncultured_genome_RUG12414/GCA_902778895.1_Rumen_uncultured_genome_RUG12414_protein.faa.gz. <urlopen error ftp error: [Errno ftp error] 550 GCA_902778895.1_Rumen_uncultured_genome_RUG12414_protein.faa.gz: No such file or directory>
2020-09-21 20:42:28,239 repophlan_get_microbes.py ERROR Error in downloading of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/778/895/GCA_902778895.1_Rumen_uncultured_genome_RUG12414/GCA_902778895.1_Rumen_uncultured_genome_RUG12414_protein.faa.gz <urlopen error ftp error: [Errno ftp error] 550 GCA_902778895.1_Rumen_uncultured_genome_RUG12414_protein.faa.gz: No such file or directory>
2020-09-21 20:42:28,239 repophlan_get_microbes.py ERROR Error in downloading of ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/778/895/GCA_902778895.1_Rumen_uncultured_genome_RUG12414/GCA_902778895.1_Rumen_uncultured_genome_RUG12414_protein.faa.gz: empty fna file!
Many thanks
repophlan_microbes.log
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