Closed parul-sharma closed 5 years ago
Hi @parul-sharma,
Thank you for submitting this!
Just to clarify, you are using a recent pull from GitHub? I'm not sure I can reproduce the error:
dilthey@hilbert227:dilthey/software/MetaMaps_fresh] perl downloadRefSeq.pl --seqencesOutDirectory download/refseq_parul --taxonomyOutDirectory download/taxonomy_parul --targetBranches bacteria
citations.dmp
delnodes.dmp
division.dmp
gencode.dmp
merged.dmp
names.dmp
nodes.dmp
gc.prt
readme.txt
Taxonomy downloaded and extracted into download/taxonomy_parul
Now download genomes for 24762 bacteria species (refseq).
...
Hi
Thanks for the reply. I updated the software and tried again. I ran into this error.
perl /home/parulsharma/bin/MetaMaps/downloadRefSeq.pl --seqencesOutDirectory Metamaps_dafaultDB+1/refseq --taxonomyOutDirectory Metamaps_dafaultDB+1/taxonomy --targetBranches bacteria
citations.dmp
delnodes.dmp
division.dmp
gencode.dmp
merged.dmp
names.dmp
nodes.dmp
gc.prt
readme.txt
Taxonomy downloaded and extracted into Metamaps_dafaultDB+1/taxonomy
Now download genomes for 24762 bacteria species (refseq).
1 / 24762 bacteria (Acaricomes_phytoseiuli) -- version 1 / 1: GET GCF_000376245.1_ASM37624v1_genomic.fna.gz Cannot transfer file Idle timeout (60 seconds): closing control connection
Cannot transfer file GCF_000376245.1_ASM37624v1_genomic.fna.gz: No such file or directory
Cannot transfer file GCF_000376245.1_ASM37624v1_genomic.fna.gz: No such file or directory
Net::FTP>>> Net::FTP(3.10)
Net::FTP>>> Exporter(5.72)
Net::FTP>>> Net::Cmd(3.10)
Net::FTP>>> IO::Socket::SSL(2.066)
Net::FTP>>> IO::Socket::IP(0.38)
Net::FTP>>> IO::Socket(1.38)
Net::FTP>>> IO::Handle(1.36)
Net::FTP=GLOB(0x55fc938c9160)<<< 220-
Net::FTP=GLOB(0x55fc938c9160)<<< This warning banner provides privacy and security notices consistent with
Net::FTP=GLOB(0x55fc938c9160)<<< applicable federal laws, directives, and other federal guidance for accessing
Net::FTP=GLOB(0x55fc938c9160)<<< this Government system, which includes all devices/storage media attached to
Net::FTP=GLOB(0x55fc938c9160)<<< this system. This system is provided for Government-authorized use only.
Net::FTP=GLOB(0x55fc938c9160)<<< Unauthorized or improper use of this system is prohibited and may result in
Net::FTP=GLOB(0x55fc938c9160)<<< disciplinary action and/or civil and criminal penalties. At any time, and for
Net::FTP=GLOB(0x55fc938c9160)<<< any lawful Government purpose, the government may monitor, record, and audit
Net::FTP=GLOB(0x55fc938c9160)<<< your system usage and/or intercept, search and seize any communication or data
Net::FTP=GLOB(0x55fc938c9160)<<< transiting or stored on this system. Therefore, you have no reasonable
Net::FTP=GLOB(0x55fc938c9160)<<< expectation of privacy. Any communication or data transiting or stored on this
Net::FTP=GLOB(0x55fc938c9160)<<< system may be disclosed or used for any lawful Government purpose.
Net::FTP=GLOB(0x55fc938c9160)<<< 220 FTP Server ready.
Net::FTP=GLOB(0x55fc938c9160)>>> USER anonymous
Net::FTP=GLOB(0x55fc938c9160)<<< 331 Anonymous login ok, send your complete email address as your password
Net::FTP=GLOB(0x55fc938c9160)>>> PASS ....
Net::FTP=GLOB(0x55fc938c9160)<<< 230 Anonymous access granted, restrictions apply
Net::FTP=GLOB(0x55fc938c9160)>>> TYPE I
Net::FTP=GLOB(0x55fc938c9160)<<< 200 Type set to I
Attempt 2 to get GCF_000376245.1_ASM37624v1_genomic.fna.gz failed at /home/parulsharma/bin/MetaMaps/downloadRefSeq.pl line 178.
Sorry I'm new at this and I really appreciate your help. Thanks
So I loaded the dependencies (zlib, boost, python) again and it worked this time. But it throws an error after 67/24762 as shown below. I have tried it 3 times again but it shows the same error.
I feel like this has something to do with the NCBI server issues but is there a way to resolve this?
This is the error:
65 / 24762 bacteria (Acidovorax_sp._KKS102) -- version 1 / 1: GET GCF_000302535.1_ASM30253v1_protein.faa.gz
65 / 24762 bacteria (Acidovorax_sp._KKS102) -- version 1 / 1: GET GCF_000302535.1_ASM30253v1_assembly_report.txt
66 / 24762 bacteria (Acidovorax_sp._MR-S7) -- version 1 / 1: GET GCF_000400995.2_ASM40099v2_genomic.fna.gz
66 / 24762 bacteria (Acidovorax_sp._MR-S7) -- version 1 / 1: GET GCF_000400995.2_ASM40099v2_genomic.gff.gz
66 / 24762 bacteria (Acidovorax_sp._MR-S7) -- version 1 / 1: GET GCF_000400995.2_ASM40099v2_protein.faa.gz
66 / 24762 bacteria (Acidovorax_sp._MR-S7) -- version 1 / 1: GET GCF_000400995.2_ASM40099v2_assembly_report.txt
67 / 24762 bacteria (Acidovorax_sp._NO-1) -- version 1 / 1: GET GCF_000238595.1_ASM23859v2_genomic.fna.gz
67 / 24762 bacteria (Acidovorax_sp._NO-1) -- version 1 / 1: GET GCF_000238595.1_ASM23859v2_genomic.gff.gz
67 / 24762 bacteria (Acidovorax_sp._NO-1) -- version 1 / 1: GET GCF_000238595.1_ASM23859v2_protein.faa.gz
67 / 24762 bacteria (Acidovorax_sp._NO-1) -- version 1 / 1: GET GCF_000238595.1_ASM23859v2_assembly_report.txt
Cannot change working directory (assembly_version) README.txt: No such file or directory
@parul-sharma OK, thank you! I think I can reproduce this error. I'll fix this ASAP, but it might take until next week.
This should be fixed now. You can also call the script with --skipIncompleteGenomes 1
if you want to speed up the process by downloading only complete genomes.
Hi
I want to add a new genome to the existing database. So far I had been using the default miniSeq database provided along the software. I have executed step 3 from the steps of construction. But I think it is required for the database to be constructed from scratch for the following step to work. Therefore, I started from the top with step 1 and got the following output. [screenshot included] It says that 0 genomes were downloaded for the bacteria branch. And I wonder why?
Thanks in advance for the help. Best regards Parul