search

molgenis / vip

Variant Interpretation Pipeline
https://molgenis.github.io/vip/
GNU Lesser General Public License v3.0
23 stars 5 forks source link

support GRCh37 and T2T inputs #529

Closed dennishendriksen closed 10 months ago

dennishendriksen commented 11 months ago 
running tests ...
cram/complex                             | KAPUTT | 171210=failed    test/output/cram/complex/.nxf.log
cram/multiproject                        | PASSED | 171211=completed test/output/cram/multiproject/.nxf.log
cram/nanopore_duo                        | PASSED | 171212=completed test/output/cram/nanopore_duo/.nxf.log
cram/nanopore                            | PASSED | 171213=completed test/output/cram/nanopore/.nxf.log
cram/single                              | PASSED | 171214=completed test/output/cram/single/.nxf.log
cram/trio                                | PASSED | 171215=completed test/output/cram/trio/.nxf.log
fastq/nanopore                           | PASSED | 171216=completed test/output/fastq/nanopore/.nxf.log
fastq/pacbio_hifi                        | PASSED | 171217=completed test/output/fastq/pacbio_hifi/.nxf.log
gvcf/liftover                            | PASSED | 171218=completed test/output/gvcf/liftover/.nxf.log
gvcf/multiproject                        | PASSED | 171219=completed test/output/gvcf/multiproject/.nxf.log
gvcf/trio                                | PASSED | 171220=completed test/output/gvcf/trio/.nxf.log
vcf/corner_cases                         | PASSED | 171221=completed test/output/vcf/corner_cases/.nxf.log
vcf/empty_input                          | PASSED | 171222=completed test/output/vcf/empty_input/.nxf.log
vcf/empty_output_filter_samples          | PASSED | 171223=completed test/output/vcf/empty_output_filter_samples/.nxf.log
vcf/empty_output_filter                  | PASSED | 171224=completed test/output/vcf/empty_output_filter/.nxf.log
vcf/filter_samples                       | PASSED | 171225=completed test/output/vcf/filter_samples/.nxf.log
vcf/liftover                             | PASSED | 171226=completed test/output/vcf/liftover/.nxf.log
vcf/multiproject_classify                | PASSED | 171227=completed test/output/vcf/multiproject_classify/.nxf.log
vcf/trio                                 | PASSED | 171228=completed test/output/vcf/trio/.nxf.log
vcf/vkgl_lb                              | PASSED | 171229=completed test/output/vcf/vkgl_lb/.nxf.log
vcf/vkgl_lp                              | PASSED | 171230=completed test/output/vcf/vkgl_lp/.nxf.log
done

cram/complex fails with error:

Checking the headers and starting positions of 2 files
Writing to .GHOPPp
Lines   total/split/realigned/skipped:  989248/0/0/0
Merging 989248 temporary files
[E::hts_open_format] Failed to open file ".GHOPPp/131070.bcf" : No file descriptors available
Could not read .GHOPPp/131070.bcf: No file descriptors available
Cleaning

while running process nf-cram_snv_deepvariant_concat_gvcfs_