Comments (7)
Mike;
This is the error message that the Broad FTP server reports when it's overloaded. I don't believe anything has changed, it's just that it doesn't handle high loads very well. We don't have a good fix for this short of hosting ourselves so the best recommendation is to retry and hopefully it'll be less stressed and work cleanly. Hope this helps.
from cloudbiolinux.
Hi Mike,
Sorry about that, there isn't much we can do about it unfortunately. It should eventually work when the servers stop being overwhelmed.
from cloudbiolinux.
See related GATK thread: https://gatkforums.broadinstitute.org/gatk/discussion/1215/how-can-i-access-the-gsa-public-ftp-server
from cloudbiolinux.
Thanks Brad, I thought that might be what was going on. I wasn't sure though because I could log into the FTP server with an external client and list the files; I was only seeing errors with the Python script.
from cloudbiolinux.
A couple of days later, I'm still seeing this error:
Running GGD recipe: hg38 1000g_snps 20160105
--2019-11-26 08:44:02-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/hg38//1000G_p$
ase1.snps.high_confidence.hg38.vcf.gz
=> ‘variation/1000G_phase1.snps.high_confidence.vcf.gz’
Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.70.223
Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.70.223|:21... connected.
Logging in as gsapubftp-anonymous ...
Login incorrect.
from cloudbiolinux.
Following up, on a fresh bcbio-nextgen 1.1.9 install, I'm still seeing this:
--2019-12-13 09:40:53-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/hg38//Mills_and_1000G_
gold_standard.indels.hg38.vcf.gz.tbi
=> ‘variation/Mills_and_1000G_gold_standard.indels.vcf.gz.tbi’
Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.70.223
Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.70.223|:21... connected.
Logging in as gsapubftp-anonymous ...
Login incorrect.
Upgrading bcbio
Upgrading bcbio-nextgen data files
List of genomes to get (from the config file at '{'genomes': [{'dbkey': 'hg38', 'name': 'Human (hg38) full', 'inde
xes': ['seq', 'twobit', 'bwa', 'hisat2'], 'annotations': ['transcripts', 'RADAR', 'rmsk', 'salmon-decoys', 'fusion
-blacklist', 'ccds', 'capture_regions', 'coverage', 'prioritize', 'dbsnp', 'hapmap_snps', '1000g_omni_snps', 'ACMG
56_genes', '1000g_snps', 'mills_indels', '1000g_indels', 'clinvar', 'qsignature', 'genesplicer', 'effects_transcri
pts', 'varpon', 'vcfanno', 'viral'], 'validation': ['giab-NA12878', 'giab-NA24385', 'giab-NA24631', 'platinum-geno
me-NA12878', 'giab-NA12878-remap', 'giab-NA12878-crossmap', 'dream-syn4-crossmap', 'dream-syn3-crossmap', 'giab-NA
12878-NA24385-somatic', 'giab-NA24143', 'giab-NA24149']}, {'dbkey': 'mm10', 'name': 'Mouse (mm10)', 'indexes': ['s
eq', 'twobit'], 'annotations': ['transcripts', 'rmsk', 'problem_regions', 'dbsnp', 'vcfanno']}, {'dbkey': 'rn6', '
name': 'Rat (rn6)', 'indexes': ['seq', 'twobit'], 'annotations': ['transcripts']}, {'dbkey': 'canFam3', 'name': 'D
og (canFam3)', 'indexes': ['twobit'], 'annotations': ['transcripts', 'dbsnp']}, {'dbkey': 'BDGP6', 'name': 'D mela
ngogaster (BDGP6)', 'indexes': ['seq'], 'annotations': ['transcripts']}], 'genome_indexes': ['bowtie2', 'rtg', 'st
ar'], 'install_liftover': False, 'install_uniref': False}'): Human (hg38) full, Mouse (mm10), Rat (rn6), Dog (canF
am3), D melangogaster (BDGP6)
Running GGD recipe: hg38 seq 1000g-20150219_1
Moving on to next genome prep method after trying ggd
GGD recipe not available for hg38 bowtie2
Downloading genome from s3: hg38 bowtie2
Moving on to next genome prep method after trying s3
No pre-computed indices for hg38 bowtie2
Preparing genome hg38 with index bowtie2
Moving on to next genome prep method after trying ggd
GGD recipe not available for hg38 rtg
Downloading genome from s3: hg38 rtg
Moving on to next genome prep method after trying s3
No pre-computed indices for hg38 rtg
Preparing genome hg38 with index rtg
Moving on to next genome prep method after trying ggd
GGD recipe not available for hg38 star
Downloading genome from s3: hg38 star
Moving on to next genome prep method after trying s3
No pre-computed indices for hg38 star
Preparing genome hg38 with index star
hg38 detected, building a simple reference with no alts, decoys or HLA from /data00/n/app/bcbio/1.1.9/install/geno
mes/Hsapiens/hg38/seq/hg38.fa to /data00/n/app/bcbio/1.1.9/install/genomes/Hsapiens/hg38/seq/hg38-simple.fa.
Preparing STAR index from /data00/n/app/bcbio/1.1.9/install/genomes/Hsapiens/hg38/seq/hg38-simple.fa.
Removing /data00/n/app/bcbio/1.1.9/install/genomes/Hsapiens/hg38/seq/hg38-simple.fa.
Running GGD recipe: hg38 transcripts 2018-10-10_92
Running GGD recipe: hg38 RADAR v2-20180202
Running GGD recipe: hg38 rmsk 20180319
Running GGD recipe: hg38 salmon-decoys 94
Running GGD recipe: hg38 fusion-blacklist 2
Running GGD recipe: hg38 ccds r20
Running GGD recipe: hg38 capture_regions 20161202
Running GGD recipe: hg38 coverage 2018-10-16
Running GGD recipe: hg38 prioritize 20181227
Running GGD recipe: hg38 dbsnp 151-20180418
Running GGD recipe: hg38 hapmap_snps 20160105
Running GGD recipe: hg38 1000g_omni_snps 20160105
Running GGD recipe: hg38 ACMG56_genes 20160726
Running GGD recipe: hg38 1000g_snps 20160105
Running GGD recipe: hg38 mills_indels 20160105
Traceback (most recent call last): [3/97495]
File "/n/app/bcbio/stable/tools/bin/bcbio_nextgen.py", line 228, in <module>
install.upgrade_bcbio(kwargs["args"])
File "/n/app/bcbio/1.1.9/install/anaconda/lib/python3.6/site-packages/bcbio/install.py", line 106, in upgrade_bcbio
upgrade_bcbio_data(args, REMOTES)
File "/n/app/bcbio/1.1.9/install/anaconda/lib/python3.6/site-packages/bcbio/install.py", line 369, in upgrade_bcbio_data
args.cores, ["ggd", "s3", "raw"])
File "/mnt/resource/tmp.1YauZ8ZyEP/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 354,
in install_data_local
_prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir)
File "/mnt/resource/tmp.1YauZ8ZyEP/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480,
in _prep_genomes
retrieve_fn(env, manager, gid, idx)
File "/mnt/resource/tmp.1YauZ8ZyEP/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 872,
in _install_with_ggd
ggd.install_recipe(os.getcwd(), env.system_install, recipe_file, gid)
File "/mnt/resource/tmp.1YauZ8ZyEP/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 30, in in
stall_recipe
recipe["recipe"]["full"]["recipe_type"], system_install)
File "/mnt/resource/tmp.1YauZ8ZyEP/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 62, in _r
un_recipe
subprocess.check_output(["bash", run_file])
File "/n/app/bcbio/1.1.9/install/anaconda/lib/python3.6/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/n/app/bcbio/1.1.9/install/anaconda/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bash', '/data00/n/app/bcbio/1.1.9/install/genomes/Hsapiens/hg38/txtmp/gg
d-run.sh']' returned non-zero exit status 6.
from cloudbiolinux.
Thanks, it will be random that this happens unfortunately.
from cloudbiolinux.
Related Issues (20)
- gnomad exome issue HOT 5
- Error while adding reference to the given genome to the base index file HOT 1
- Failed to install due to broken link HOT 5
- Feature request: Update Drosophila genome build to support dm6 HOT 5
- mirbase GFF file not installed for mmu even if it is present HOT 2
- a peculiar bug in grch37 dbnsftp recipe HOT 3
- gnomad_exome ggb randomly fails on chr1 HOT 5
- UNPACK_DIR: unbound variable HOT 3
- Issues with installing dbscSNV HOT 7
- bismark_indices.loc missing HOT 2
- Problems with centralized conda installation HOT 2
- Integrate additional GiaB samples for validation HOT 1
- limit conda environments HOT 1
- tar -p option causes quota issues in case quota are enforced on group level HOT 3
- Don't use both mamba and conda to install packages
- Incorrect Ensembl release version for hg38 transcripts.yaml
- Installation problem conda package libtiff HOT 1
- Please submit cloudbiolinux/BCBIO related issues to bcbio github
- cloubiolinux.org website is hijacked or domain expired
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