Failing weekly tests

[bernt-matthias]

List of currently failing weekly tests:

Triaged

• data_manager_omamer different than expected, difference (param_dict?) Fix and update the omamer DM #7828 omamer datamanager broken #6585
• picard_index_builder_data_manager empty json
• kraken2_build_database @ERROR: Unknown module 'pub'
• tools/beacon2-import/ all fail due to ServerSelectionTimeoutError: 20.108.51.167:27017
• tools/chewbbaca different than expected Chewbacca fixes #7824
• tools/cialign Expected file size of 63k+-3k found 66238 CIAlign: Fix weekly failing test #7725
• tools/comebin_bam Expected file size of 17000+-1000 found 289491
• tools/commet Expected file size of 1k+-0 found 13120
• tools/concoct Expected file size of 362924+-10 found 362698
• tools/delly Job in error state..
• tools/disco Expected text 'FIRST LOOP ITERATION 1' in output
• tools/fastq_dl Expected file size of 23102+-0 found 104300
• tools/fermikit make: command not found
• tools/ggplot2/ggplot_histogram.xml Expected file size of 10k+-1k found 108160
• tools/homer diff
• tools/idr_download Expected file size of 2097286+-0 found 2097408
• tools/interval2maf/ diff
• tools/khmer Expected file size of 1k+-0 found 20000008
• tools/lofreq_call diff
• tools/lumpy_sv/lumpy_preprocessing.xml diff SAM PG lines
• tools/medaka Job in error state..
• tools/megahit Expected line matching expression
• tools/metaphlan Expected file size of 11869+-0 found 11911
• tools/metasbt Expected file size of 468556+-10000 found 442867
• tools/mg_toolkit Expected file size of 15684535+-0 found 78038108
• tools/mothur Job in error state.., Timeout, diff checksum, metadata verification
• tools/ncbi_entrez_eutils/ diff
• tools/ngmlr diff
• tools/openalex [!] Error: This work has no citing papers. should be an exit code
• tools/pangolin (Test # 2) Job in error state.. Fix pangolin  #7676
• tools/pgxRpi/ DIFFICULT add pgxRpi tool  #6805 (comment)
• tools/plasmidfinder Fix linter problems for Plasmidfinder #7669
• tools/pyega3 (Test # 2) diff
• tools/pysradb Expected file size of 82507+-10000 found 71230
• tools/query_impc/ diff
• tools/repeatmasker Species "rattus" is not known to RepeatMasker WIP repeatmasker: bump and dfam data table #6845
• tools/rp2biosensor gzip.BadGzipFile: Not a gzipped file
• tools/rptools/rptools_rpextractsink gzip.BadGzipFile: Not a gzipped file
• tools/sarscov2formatter produces no output
• tools/scpipe "en_US.UTF-8" cannot be honored + Aborted (core dumped)
• tools/selenzy_wrapper diff 1 line
• tools/sickle (Test # 7) diff + 4 lines
• tools/simple_weather (Test # 1) different
• tools/spotyping (Test # 3) Expected text 'Spoligotype' in output ('') + exit code 1
• tools/staramr bump staramr container BioContainers/multi-package-containers#3860
• tools/trinity Rscript results.matrix.R died with ret 256
• tools/trinotate downloads uniprot + wget "http://eggnogdb.embl.de/download/eggnog_4.5/data/NOG/NOG.annotations.tsv.gz" died with ret 2048

Timeout

• diffdock (Test # 1)

Temporary problems?:

• dada2_removeBimeraDenovo (R: command not found)