germlines/{split-germlines.py,ncbi.py}: keep track of the position of retrieven up/downstreams

see #4656
22 jobs for feature-a/4271-update-germlines in 3 minutes and 44 seconds (queued for 1 minute and 46 seconds)
Status Job ID Name Coverage
  Test Tools
passed #939492
test_tools

00:00:11

 
  Test Quality
failed #939493
allowed to fail
code_quality

00:00:05

 
  Test Unit
failed #939494
test_algo_unit

00:03:27

 
  Test Functional
skipped #939495
test_algo_should
 
  Test Shouldvdj
skipped #939496
test_algo_shouldvdj
 
  Coverage
skipped #939497
algo_coverage
 
  Prepare Release
skipped #939498
allowed to fail manual
prepare_release
 
  Valgrind Unit
skipped #939499
valgrind
algo_valgrind_unit
 
  Valgrind Functional
skipped #939500
valgrind allowed to fail manual
algo_valgrind_functional
 
  Multiple Tests
skipped #939508
cidocker allowed to fail manual
test_clang34_manual
skipped #939509
cidocker allowed to fail manual
test_clang4_manual
skipped #939510
cidocker allowed to fail manual
test_clang6_manual
skipped #939511
cidocker allowed to fail manual
test_clang7_manual
skipped #939507
cidocker allowed to fail manual
test_gcc10_manual
skipped #939501
cidocker allowed to fail manual
test_gcc48_manual
skipped #939502
cidocker allowed to fail manual
test_gcc5_manual
skipped #939503
cidocker allowed to fail manual
test_gcc6_manual
skipped #939504
cidocker allowed to fail manual
test_gcc7_manual
skipped #939505
cidocker allowed to fail manual
test_gcc8_manual
skipped #939506
cidocker allowed to fail manual
test_gcc9_manual
 
  Benchmark
skipped #939513
cidocker allowed to fail manual
benchmark_algo
skipped #939512
cidocker allowed to fail manual
profiling_algo
 
Name Stage Failure
failed
test_algo_unit Test Unit
make[2]: *** [test] Aborted
make[2]: Leaving directory '/home/gitlab-runner/builds/b8d876c1/0/vidjil/vidjil/algo/tests'
Makefile:174: recipe for target 'unit' failed
make[1]: *** [unit] Error 2
make[1]: Leaving directory '/home/gitlab-runner/builds/b8d876c1/0/vidjil/vidjil/algo'
Makefile:209: recipe for target 'unit_coverage' failed
make: *** [unit_coverage] Error 2
make: Leaving directory '/home/gitlab-runner/builds/b8d876c1/0/vidjil/vidjil/algo'
ERROR: Job failed: exit status 1
failed
code_quality Test Quality
$ function propagate_env_vars() { # collapsed multi-line command
$ docker pull --quiet "$CODE_QUALITY_IMAGE"
unknown flag: --quiet
See 'docker pull --help'.
Uploading artifacts...
Runtime platform arch=386 os=linux pid=3745 revision=58272c27 version=12.7.0
WARNING: gl-code-quality-report.json: no matching files
ERROR: No files to upload
ERROR: Job failed: exit status 1