[2024-01-24 14:21:47,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:47,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:47,308] [INFO] DQC Reference Directory: /var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference
[2024-01-24 14:21:48,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:48,593] [INFO] Task started: Prodigal
[2024-01-24 14:21:48,593] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf83b1cf-3423-446d-9699-3d608837eeec/GCF_014207795.1_ASM1420779v1_genomic.fna.gz | prodigal -d GCF_014207795.1_ASM1420779v1_genomic.fna/cds.fna -a GCF_014207795.1_ASM1420779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:11,462] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:11,463] [INFO] Task started: HMMsearch
[2024-01-24 14:22:11,463] [INFO] Running command: hmmsearch --tblout GCF_014207795.1_ASM1420779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference/reference_markers.hmm GCF_014207795.1_ASM1420779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:11,863] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:11,864] [INFO] Found 6/6 markers.
[2024-01-24 14:22:11,932] [INFO] Query marker FASTA was written to GCF_014207795.1_ASM1420779v1_genomic.fna/markers.fasta
[2024-01-24 14:22:11,933] [INFO] Task started: Blastn
[2024-01-24 14:22:11,933] [INFO] Running command: blastn -query GCF_014207795.1_ASM1420779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference/reference_markers.fasta -out GCF_014207795.1_ASM1420779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:13,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:13,219] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:13,220] [INFO] Target genome list was writen to GCF_014207795.1_ASM1420779v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:13,225] [INFO] Task started: fastANI
[2024-01-24 14:22:13,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf83b1cf-3423-446d-9699-3d608837eeec/GCF_014207795.1_ASM1420779v1_genomic.fna.gz --refList GCF_014207795.1_ASM1420779v1_genomic.fna/target_genomes.txt --output GCF_014207795.1_ASM1420779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:42,086] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:42,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:42,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:42,108] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:42,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:42,109] [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 sandramycini	strain=DSM 15626	GCA_014207795.1	60450	60450	type	True	100.0	2705	2706	95	conclusive
Kribbella sandramycini	strain=ATCC 39419	GCA_013131805.1	60450	60450	type	True	99.9925	2686	2706	95	conclusive
Kribbella antibiotica	strain=JCM 13523	GCA_004349055.1	190195	190195	type	True	84.6019	1882	2706	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	83.5709	1444	2706	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	83.3865	1596	2706	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	83.3479	1656	2706	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	83.2914	1593	2706	95	below_threshold
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	83.2714	1609	2706	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	83.1726	1654	2706	95	below_threshold
Kribbella pittospori	strain=NRRL B-24813	GCA_004331465.1	722689	722689	type	True	83.1703	1637	2706	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	83.1594	1623	2706	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	83.0888	1575	2706	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	83.0158	1536	2706	95	below_threshold
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	82.8795	1650	2706	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.0298	559	2706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:42,111] [INFO] DFAST Taxonomy check result was written to GCF_014207795.1_ASM1420779v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:42,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:42,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:42,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference/checkm_data
[2024-01-24 14:22:42,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:42,186] [INFO] Task started: CheckM
[2024-01-24 14:22:42,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207795.1_ASM1420779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207795.1_ASM1420779v1_genomic.fna/checkm_input GCF_014207795.1_ASM1420779v1_genomic.fna/checkm_result
[2024-01-24 14:23:57,683] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:57,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:57,708] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:57,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:57,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207795.1_ASM1420779v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:57,709] [INFO] Task started: Blastn
[2024-01-24 14:23:57,709] [INFO] Running command: blastn -query GCF_014207795.1_ASM1420779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9707988-7461-4968-a2c3-39d09db6e012/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207795.1_ASM1420779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:59,810] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:59,813] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:59,813] [INFO] Target genome list was writen to GCF_014207795.1_ASM1420779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:59,823] [INFO] Task started: fastANI
[2024-01-24 14:23:59,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf83b1cf-3423-446d-9699-3d608837eeec/GCF_014207795.1_ASM1420779v1_genomic.fna.gz --refList GCF_014207795.1_ASM1420779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207795.1_ASM1420779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:32,272] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:32,290] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:32,291] [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_013131805.1	s__Kribbella sandramycini	99.9925	2686	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004348455.1	s__Kribbella albertanoniae	85.2274	1860	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349055.1	s__Kribbella antibiotica	84.586	1885	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331485.1	s__Kribbella sp004331485	83.4161	1591	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761605.1	s__Kribbella shirazensis	83.3179	1587	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331345.1	s__Kribbella soli	83.2691	1609	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342025.1	s__Kribbella sp004342025	83.2151	1636	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216905.1	s__Kribbella sp004216905	83.194	1603	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331465.1	s__Kribbella pittospori	83.1756	1637	2706	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	83.1031	1529	2706	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	83.0507	1574	2706	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	83.0482	1580	2706	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	83.0454	1530	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365355.1	s__Kribbella sp004365355	82.9979	1566	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365875.1	s__Kribbella sp004365875	82.9671	1598	2706	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984195.1	s__Kribbella sp001984195	82.7969	1528	2706	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 14:24:32,293] [INFO] GTDB search result was written to GCF_014207795.1_ASM1420779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:32,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:32,297] [INFO] DFAST_QC result json was written to GCF_014207795.1_ASM1420779v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:32,298] [INFO] DFAST_QC completed!
[2024-01-24 14:24:32,298] [INFO] Total running time: 0h2m45s