[2024-01-24 11:44:22,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:22,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:22,883] [INFO] DQC Reference Directory: /var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference
[2024-01-24 11:44:26,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,344] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg30f2c3e8-8636-4417-abaa-61880fb82990/GCF_013127955.1_ASM1312795v1_genomic.fna.gz | prodigal -d GCF_013127955.1_ASM1312795v1_genomic.fna/cds.fna -a GCF_013127955.1_ASM1312795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:52,040] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:52,040] [INFO] Task started: HMMsearch
[2024-01-24 11:44:52,040] [INFO] Running command: hmmsearch --tblout GCF_013127955.1_ASM1312795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference/reference_markers.hmm GCF_013127955.1_ASM1312795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:52,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:52,368] [INFO] Found 6/6 markers.
[2024-01-24 11:44:52,419] [INFO] Query marker FASTA was written to GCF_013127955.1_ASM1312795v1_genomic.fna/markers.fasta
[2024-01-24 11:44:52,419] [INFO] Task started: Blastn
[2024-01-24 11:44:52,420] [INFO] Running command: blastn -query GCF_013127955.1_ASM1312795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference/reference_markers.fasta -out GCF_013127955.1_ASM1312795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:53,034] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:53,046] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:53,047] [INFO] Target genome list was writen to GCF_013127955.1_ASM1312795v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:53,057] [INFO] Task started: fastANI
[2024-01-24 11:44:53,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f2c3e8-8636-4417-abaa-61880fb82990/GCF_013127955.1_ASM1312795v1_genomic.fna.gz --refList GCF_013127955.1_ASM1312795v1_genomic.fna/target_genomes.txt --output GCF_013127955.1_ASM1312795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:20,041] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:20,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:20,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:20,069] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:20,070] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:20,070] [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
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	100.0	1906	1906	95	conclusive
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.9063	467	1906	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.7717	577	1906	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.7594	543	1906	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.618	495	1906	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.5923	554	1906	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.5022	510	1906	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.4647	451	1906	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.4575	387	1906	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	77.4216	525	1906	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.376	496	1906	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.3562	397	1906	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	77.3453	514	1906	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.3375	347	1906	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.2504	406	1906	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	77.2454	434	1906	95	below_threshold
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	76.3097	224	1906	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.2688	281	1906	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	76.0942	225	1906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:20,072] [INFO] DFAST Taxonomy check result was written to GCF_013127955.1_ASM1312795v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:20,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:20,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:20,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference/checkm_data
[2024-01-24 11:45:20,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:20,132] [INFO] Task started: CheckM
[2024-01-24 11:45:20,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013127955.1_ASM1312795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013127955.1_ASM1312795v1_genomic.fna/checkm_input GCF_013127955.1_ASM1312795v1_genomic.fna/checkm_result
[2024-01-24 11:46:31,999] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:32,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:32,021] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:32,022] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:32,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013127955.1_ASM1312795v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:32,022] [INFO] Task started: Blastn
[2024-01-24 11:46:32,023] [INFO] Running command: blastn -query GCF_013127955.1_ASM1312795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0149462-a1db-435c-9c72-cd6ae98d08f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013127955.1_ASM1312795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:32,845] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:32,849] [INFO] Selected 19 target genomes.
[2024-01-24 11:46:32,849] [INFO] Target genome list was writen to GCF_013127955.1_ASM1312795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:32,863] [INFO] Task started: fastANI
[2024-01-24 11:46:32,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f2c3e8-8636-4417-abaa-61880fb82990/GCF_013127955.1_ASM1312795v1_genomic.fna.gz --refList GCF_013127955.1_ASM1312795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013127955.1_ASM1312795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:57,351] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:57,368] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:57,369] [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_013127955.1	s__Spirosoma taeanense	100.0	1906	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011604685.1	s__Spirosoma aureum	77.9197	467	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.763	576	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_002067135.1	s__Spirosoma rigui	77.7599	545	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849055.1	s__Spirosoma sp012849055	77.6299	504	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	77.618	495	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870035.1	s__Spirosoma lacussanchae	77.5866	555	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001988955.1	s__Spirosoma montaniterrae	77.5578	477	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003259005.1	s__Spirosoma sp003259005	77.5563	399	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900230225.1	s__Spirosoma fluviale	77.5083	509	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974425.1	s__Spirosoma radiotolerans	77.4924	451	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699035.1	s__Spirosoma validum	77.4503	388	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282275.1	s__Spirosoma utsteinense	77.4216	525	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
GCF_003583365.1	s__Fibrisoma montanum	77.4025	553	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	77.3761	496	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699005.1	s__Spirosoma profusum	77.3488	398	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754945.1	s__Spirosoma sp009754945	77.3375	347	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	77.2434	407	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374065.1	s__Spirosoma luteum	77.1208	422	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:57,370] [INFO] GTDB search result was written to GCF_013127955.1_ASM1312795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:57,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:57,379] [INFO] DFAST_QC result json was written to GCF_013127955.1_ASM1312795v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:57,379] [INFO] DFAST_QC completed!
[2024-01-24 11:46:57,379] [INFO] Total running time: 0h2m34s