[2024-01-24 13:40:43,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference
[2024-01-24 13:40:44,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,914] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg04f93373-c718-4a80-bc35-59f3e5b225b0/GCF_004342085.1_ASM434208v1_genomic.fna.gz | prodigal -d GCF_004342085.1_ASM434208v1_genomic.fna/cds.fna -a GCF_004342085.1_ASM434208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:12,700] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:12,701] [INFO] Task started: HMMsearch
[2024-01-24 13:41:12,701] [INFO] Running command: hmmsearch --tblout GCF_004342085.1_ASM434208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference/reference_markers.hmm GCF_004342085.1_ASM434208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:13,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:13,203] [INFO] Found 6/6 markers.
[2024-01-24 13:41:13,290] [INFO] Query marker FASTA was written to GCF_004342085.1_ASM434208v1_genomic.fna/markers.fasta
[2024-01-24 13:41:13,290] [INFO] Task started: Blastn
[2024-01-24 13:41:13,290] [INFO] Running command: blastn -query GCF_004342085.1_ASM434208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference/reference_markers.fasta -out GCF_004342085.1_ASM434208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:14,638] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:14,641] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:14,642] [INFO] Target genome list was writen to GCF_004342085.1_ASM434208v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:14,648] [INFO] Task started: fastANI
[2024-01-24 13:41:14,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f93373-c718-4a80-bc35-59f3e5b225b0/GCF_004342085.1_ASM434208v1_genomic.fna.gz --refList GCF_004342085.1_ASM434208v1_genomic.fna/target_genomes.txt --output GCF_004342085.1_ASM434208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:44,604] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:44,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:44,617] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:44,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:44,618] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Kribbella catacumbae	strain=DSM 19601	GCA_000372465.1	460086	460086	type	True	84.7879	1717	3026	95	below_threshold
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	84.051	1592	3026	95	below_threshold
Kribbella monticola	strain=NEAU-SW521	GCA_003261635.1	2185285	2185285	type	True	83.7909	1695	3026	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	83.739	1671	3026	95	below_threshold
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	83.6057	1689	3026	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	83.4192	1513	3026	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	83.1923	1724	3026	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	82.4719	1631	3026	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	82.4251	1618	3026	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	82.4091	1640	3026	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	82.4026	1504	3026	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	82.3527	1665	3026	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	82.2601	1485	3026	95	below_threshold
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	81.769	1343	3026	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.8008	574	3026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,620] [INFO] DFAST Taxonomy check result was written to GCF_004342085.1_ASM434208v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:44,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:44,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:44,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference/checkm_data
[2024-01-24 13:41:44,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:44,706] [INFO] Task started: CheckM
[2024-01-24 13:41:44,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342085.1_ASM434208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342085.1_ASM434208v1_genomic.fna/checkm_input GCF_004342085.1_ASM434208v1_genomic.fna/checkm_result
[2024-01-24 13:43:01,423] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:01,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:01,453] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:01,453] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:01,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342085.1_ASM434208v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:01,454] [INFO] Task started: Blastn
[2024-01-24 13:43:01,454] [INFO] Running command: blastn -query GCF_004342085.1_ASM434208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2184cbe5-4843-4b09-920b-fa5b2ad15770/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342085.1_ASM434208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:03,353] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:03,356] [INFO] Selected 13 target genomes.
[2024-01-24 13:43:03,356] [INFO] Target genome list was writen to GCF_004342085.1_ASM434208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:03,416] [INFO] Task started: fastANI
[2024-01-24 13:43:03,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f93373-c718-4a80-bc35-59f3e5b225b0/GCF_004342085.1_ASM434208v1_genomic.fna.gz --refList GCF_004342085.1_ASM434208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342085.1_ASM434208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:29,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:29,522] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:29,522] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004345365.1	s__Kribbella sp004345365	95.2984	2465	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.33	95.31	0.84	0.84	3	conclusive
GCF_000372465.1	s__Kribbella catacumbae	84.7731	1720	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548305.1	s__Kribbella sp010548305	84.6594	1682	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365175.1	s__Kribbella sp004365175	84.0949	1702	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217565.1	s__Kribbella qitaiheensis	84.0558	1676	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024345.1	s__Kribbella flavida	84.0524	1592	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361855.1	s__Kribbella sp004361855	83.8695	1798	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261635.1	s__Kribbella monticola	83.7841	1696	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828865.1	s__Kribbella amoyensis	83.7258	1674	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345665.1	s__Kribbella sp004345665	83.0182	1681	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	82.3634	1512	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715085.1	s__Kribbella jejuensis	82.2404	1488	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217145.1	s__Kribbella soli_A	82.1368	1658	3026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:29,524] [INFO] GTDB search result was written to GCF_004342085.1_ASM434208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:29,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:29,528] [INFO] DFAST_QC result json was written to GCF_004342085.1_ASM434208v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:29,528] [INFO] DFAST_QC completed!
[2024-01-24 13:43:29,528] [INFO] Total running time: 0h2m46s