[2024-01-24 12:37:08,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:08,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:08,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference
[2024-01-24 12:37:09,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:09,789] [INFO] Task started: Prodigal
[2024-01-24 12:37:09,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c8db756-5e04-4b52-aaea-6cd7fe0f001c/GCF_003073135.1_ASM307313v1_genomic.fna.gz | prodigal -d GCF_003073135.1_ASM307313v1_genomic.fna/cds.fna -a GCF_003073135.1_ASM307313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:26,160] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:26,161] [INFO] Task started: HMMsearch
[2024-01-24 12:37:26,161] [INFO] Running command: hmmsearch --tblout GCF_003073135.1_ASM307313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference/reference_markers.hmm GCF_003073135.1_ASM307313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:26,486] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:26,488] [INFO] Found 6/6 markers.
[2024-01-24 12:37:26,539] [INFO] Query marker FASTA was written to GCF_003073135.1_ASM307313v1_genomic.fna/markers.fasta
[2024-01-24 12:37:26,540] [INFO] Task started: Blastn
[2024-01-24 12:37:26,540] [INFO] Running command: blastn -query GCF_003073135.1_ASM307313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference/reference_markers.fasta -out GCF_003073135.1_ASM307313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:27,610] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:27,615] [INFO] Selected 25 target genomes.
[2024-01-24 12:37:27,616] [INFO] Target genome list was writen to GCF_003073135.1_ASM307313v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:27,629] [INFO] Task started: fastANI
[2024-01-24 12:37:27,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c8db756-5e04-4b52-aaea-6cd7fe0f001c/GCF_003073135.1_ASM307313v1_genomic.fna.gz --refList GCF_003073135.1_ASM307313v1_genomic.fna/target_genomes.txt --output GCF_003073135.1_ASM307313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:53,179] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:53,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:53,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:53,199] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:53,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:53,199] [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
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	100.0	1812	1816	95	conclusive
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	88.6493	1547	1816	95	below_threshold
Euzebya tangerina	strain=F10	GCA_003074135.1	591198	591198	type	True	78.1508	548	1816	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	76.1273	323	1816	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	76.0758	274	1816	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	76.072	333	1816	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	76.0604	335	1816	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.9733	392	1816	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	75.8884	231	1816	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	75.7324	266	1816	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	75.5674	226	1816	95	below_threshold
Geodermatophilus aquaeductus	strain=DSM 46834	GCA_900182545.1	1564161	1564161	type	True	75.5319	403	1816	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	75.5161	364	1816	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	75.48	347	1816	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	75.4564	411	1816	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	75.4267	315	1816	95	below_threshold
Kineococcus aurantiacus	strain=DSM 7487	GCA_013409345.1	37633	37633	type	True	75.3882	354	1816	95	below_threshold
Pseudonocardia autotrophica	strain=NBRC 12743	GCA_003945385.1	2074	2074	suspected-type	True	75.3592	362	1816	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	75.3516	305	1816	95	below_threshold
Pseudonocardia autotrophica	strain=DSM 535	GCA_002119215.1	2074	2074	suspected-type	True	75.3458	358	1816	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	75.3273	433	1816	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	75.2936	431	1816	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	75.2846	295	1816	95	below_threshold
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	75.2821	355	1816	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	74.9741	75	1816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:53,203] [INFO] DFAST Taxonomy check result was written to GCF_003073135.1_ASM307313v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:53,204] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:53,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:53,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference/checkm_data
[2024-01-24 12:37:53,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:53,260] [INFO] Task started: CheckM
[2024-01-24 12:37:53,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003073135.1_ASM307313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003073135.1_ASM307313v1_genomic.fna/checkm_input GCF_003073135.1_ASM307313v1_genomic.fna/checkm_result
[2024-01-24 12:39:30,499] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:30,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:30,526] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:30,527] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:30,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003073135.1_ASM307313v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:30,527] [INFO] Task started: Blastn
[2024-01-24 12:39:30,527] [INFO] Running command: blastn -query GCF_003073135.1_ASM307313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e239cde-4eea-4475-b71a-3b2f5d8a6497/dqc_reference/reference_markers_gtdb.fasta -out GCF_003073135.1_ASM307313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:32,114] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:32,118] [INFO] Selected 16 target genomes.
[2024-01-24 12:39:32,118] [INFO] Target genome list was writen to GCF_003073135.1_ASM307313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:32,152] [INFO] Task started: fastANI
[2024-01-24 12:39:32,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c8db756-5e04-4b52-aaea-6cd7fe0f001c/GCF_003073135.1_ASM307313v1_genomic.fna.gz --refList GCF_003073135.1_ASM307313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003073135.1_ASM307313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:47,148] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:47,165] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:47,166] [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_003073135.1	s__Euzebya rosea	100.0	1812	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003344865.1	s__Euzebya sp003344865	88.6577	1546	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074135.1	s__Euzebya tangerina	78.1376	550	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696915.1	s__JACCXR01 sp013696915	76.4954	304	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553795.1	s__T1Sed10-49 sp003553795	76.4919	319	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	99.28	99.23	0.95	0.92	4	-
GCA_007119305.1	s__SKPY01 sp007119305	76.3718	202	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKPY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133145.1	s__T1Sed10-49 sp007133145	76.1074	202	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	98.98	98.60	0.85	0.78	3	-
GCF_004300825.1	s__Egicoccus halophilus	76.1064	333	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003558435.1	s__PWLR01 sp003558435	75.9321	213	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__PWLR01	95.0	99.63	99.63	0.94	0.94	2	-
GCF_004683965.1	s__Nocardioides seonyuensis	75.8588	212	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024385.1	s__Thermomonospora curvata	75.7292	266	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_013004605.1	s__Pseudokineococcus marinus	75.5979	220	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	75.4701	407	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	75.4205	315	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_014204975.1	s__Jiangella mangrovi	75.3186	432	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190915.1	s__Mycobacterium iranicum_B	75.2611	227	1816	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:47,167] [INFO] GTDB search result was written to GCF_003073135.1_ASM307313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:47,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:47,172] [INFO] DFAST_QC result json was written to GCF_003073135.1_ASM307313v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:47,172] [INFO] DFAST_QC completed!
[2024-01-24 12:39:47,172] [INFO] Total running time: 0h2m39s