Closed cyriltata closed 2 years ago
here is why
Command error:
--2022-05-11 13:07:33-- ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr22.fa.gz
(try:11) => ‘chr22.fa.gz’
Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:21... failed: Connection timed out.
Retrying.
Hi @cyriltata,
Does the machine you are running on have a connection to the internet? It seems like it is failing to download the reference genome for some reason. Otherwise it is possible that there was a temporary outage of the ucsc URL as well.
Hi @jemunro
Yes I am connected to the internet but using some hpc cluster so maybe there is some firewall there. However, I was able to download same file manually, placed it on our own servers then was able to proceed.
Now I get another error when executing
Error executing process > 'typing:get_pharmvar_vcf (CYP2D6:5.1.14)'
Caused by:
Process `typing:get_pharmvar_vcf (CYP2D6:5.1.14)` terminated for an unknown reason -- Likely it has been terminated by the external system
Command error:
Lines total/split/realigned/skipped: 1/0/0/0
Lines total/split/realigned/skipped: 2/0/0/0
Lines total/split/realigned/skipped: 1/0/0/0
Lines total/split/realigned/skipped: 4/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 8/0/0/0
Lines total/split/realigned/skipped: 6/0/0/0
Lines total/split/realigned/skipped: 16/0/0/0
Lines total/split/realigned/skipped: 15/0/0/0
Lines total/split/realigned/skipped: 19/0/0/0
Lines total/split/realigned/skipped: 9/0/0/0
Lines total/split/realigned/skipped: 23/0/0/0
Lines total/split/realigned/skipped: 21/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 17/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 2/0/0/0
Lines total/split/realigned/skipped: 2/0/0/0
Lines total/split/realigned/skipped: 7/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 15/0/0/0
Lines total/split/realigned/skipped: 2/0/0/0
Lines total/split/realigned/skipped: 1/0/0/0
Lines total/split/realigned/skipped: 1/0/0/0
Lines total/split/realigned/skipped: 1/0/1/0
Lines total/split/realigned/skipped: 3/0/1/0
Lines total/split/realigned/skipped: 1/0/1/0
Lines total/split/realigned/skipped: 2/0/0/0
Lines total/split/realigned/skipped: 1/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 3/0/0/0
Lines total/split/realigned/skipped: 1/0
Hi @cyriltata,
It seems like the process is either running out of time or memory.
I've just released a new version that increases the memory for this task and also adds the ability for jobs to re-execute with increased walltime and memory if they fail. Give it a go and see if it solves your problem.
@jemunro all almost ran smooth but for some MySQL connection failure but I am suspecting it may be a firewall issue at my end
Command error:
Possible precedence issue with control flow operator at /opt/conda/envs/PLASTER_22.05.01/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
DBI connect('host=ensembldb.ensembl.org;port=3306','anonymous',...) failed: Can't connect to MySQL server on 'ensembldb.ensembl.org' (110) at /opt/conda/envs/PLASTER_22.05.01/share/ensembl-vep-104.0-0/Bio/EnsEMBL/Registry.pm line 1771.
Execution state
[8d/0e5450] process > typing:prep_ref:wget [100%] 1 of 1 ✔
[eb/0292d4] process > typing:prep_ref:fai_dict [100%] 1 of 1 ✔
[99/bf386d] process > typing:get_pharmvar_vcf (5.... [100%] 1 of 1 ✔
[b0/b00347] process > typing:prep_bams:merge (NA1... [100%] 4 of 4 ✔
[7b/6a0864] process > typing:prep_bams:fusion_cal... [100%] 10 of 10 ✔
[a6/907e5f] process > typing:prep_bams:fusion_rep... [100%] 1 of 1 ✔
[c9/89e41c] process > typing:prep_bams:downsample... [100%] 2 of 2 ✔
[82/240087] process > typing:prep_bams:index (NA1... [100%] 19 of 19 ✔
[1b/9991fe] process > typing:gatk_1:haplotype_cal... [100%] 19 of 19 ✔
[d5/127fa0] process > typing:gatk_1:genotype_gvcf... [100%] 2 of 2 ✔
[b4/b6ee84] process > typing:phase:get_snp_pos (C... [100%] 2 of 2 ✔
[98/fa1ab7] process > typing:phase:assign_snps (N... [100%] 19 of 19 ✔
[ff/b33f33] process > typing:phase:amp_phaser (NA... [100%] 19 of 19 ✔
[12/1a3140] process > typing:phase:split_phases (... [100%] 16 of 16 ✔
[12/271b53] process > typing:gatk_2:haplotype_cal... [100%] 28 of 28 ✔
[78/2d8072] process > typing:gatk_2:genotype_gvcf... [100%] 2 of 2 ✔
[76/cb1677] process > typing:gatk_2:get_targ_site... [100%] 1 of 1 ✔
[f0/515288] process > typing:gatk_2:call_targ_sit... [100%] 19 of 19 ✔
[64/494ec9] process > typing:gatk_2:merge_targ_si... [100%] 1 of 1 ✔
[bd/841380] process > typing:vep (CYP2D7) [ 75%] 3 of 4, failed: 3...
[- ] process > typing:pharmvar_star_allele -
Error executing process > 'typing:vep (CYP2D7)'
@jemunro just as a follow up, could we use vep over http and not using a database connection?
vep --input_file $vcf \\
--database \\
--format vcf \\
--vcf \\
--everything \\
--allele_number \\
--variant_class \\
--dont_skip \\
--assembly $params.vep_assembly \\
--cache_version $params.vep_cache_ver \\
--allow_non_variant \\
--pick_allele_gene \\
--output_file STDOUT |
bcftools view --no-version -Oz -o $out
bcftools index -t $out
So had to set up my own local DB. It was a firewall issue
After three hours of running the test pipeline, output hangs at