[2024-01-25 18:11:35,798] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference
[2024-01-25 18:11:36,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,996] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg10fb620b-c4e0-453b-a60a-62647eb4ba81/GCF_022321465.1_ASM2232146v1_genomic.fna.gz | prodigal -d GCF_022321465.1_ASM2232146v1_genomic.fna/cds.fna -a GCF_022321465.1_ASM2232146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:49,090] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:49,090] [INFO] Task started: HMMsearch
[2024-01-25 18:11:49,090] [INFO] Running command: hmmsearch --tblout GCF_022321465.1_ASM2232146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference/reference_markers.hmm GCF_022321465.1_ASM2232146v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:49,383] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:49,384] [INFO] Found 6/6 markers.
[2024-01-25 18:11:49,426] [INFO] Query marker FASTA was written to GCF_022321465.1_ASM2232146v1_genomic.fna/markers.fasta
[2024-01-25 18:11:49,427] [INFO] Task started: Blastn
[2024-01-25 18:11:49,427] [INFO] Running command: blastn -query GCF_022321465.1_ASM2232146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference/reference_markers.fasta -out GCF_022321465.1_ASM2232146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:50,314] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:50,317] [INFO] Selected 15 target genomes.
[2024-01-25 18:11:50,317] [INFO] Target genome list was writen to GCF_022321465.1_ASM2232146v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:50,341] [INFO] Task started: fastANI
[2024-01-25 18:11:50,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg10fb620b-c4e0-453b-a60a-62647eb4ba81/GCF_022321465.1_ASM2232146v1_genomic.fna.gz --refList GCF_022321465.1_ASM2232146v1_genomic.fna/target_genomes.txt --output GCF_022321465.1_ASM2232146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:03,330] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:03,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:03,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:03,341] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:12:03,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:12:03,341] [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
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	91.2966	1190	1447	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	84.3035	991	1447	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	81.2381	774	1447	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	81.2297	762	1447	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	80.9528	764	1447	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.9523	774	1447	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.9503	782	1447	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.5896	606	1447	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.2537	662	1447	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5963	466	1447	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.3236	431	1447	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.2685	470	1447	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8814	383	1447	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.0657	300	1447	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.0412	297	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:03,342] [INFO] DFAST Taxonomy check result was written to GCF_022321465.1_ASM2232146v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:03,343] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:03,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:03,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference/checkm_data
[2024-01-25 18:12:03,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:03,386] [INFO] Task started: CheckM
[2024-01-25 18:12:03,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022321465.1_ASM2232146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022321465.1_ASM2232146v1_genomic.fna/checkm_input GCF_022321465.1_ASM2232146v1_genomic.fna/checkm_result
[2024-01-25 18:12:42,416] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:42,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:42,433] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:42,433] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:42,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022321465.1_ASM2232146v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:42,434] [INFO] Task started: Blastn
[2024-01-25 18:12:42,434] [INFO] Running command: blastn -query GCF_022321465.1_ASM2232146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdb6b510-3448-455b-924d-ef82d7903325/dqc_reference/reference_markers_gtdb.fasta -out GCF_022321465.1_ASM2232146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:43,990] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:43,994] [INFO] Selected 14 target genomes.
[2024-01-25 18:12:43,994] [INFO] Target genome list was writen to GCF_022321465.1_ASM2232146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:44,007] [INFO] Task started: fastANI
[2024-01-25 18:12:44,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg10fb620b-c4e0-453b-a60a-62647eb4ba81/GCF_022321465.1_ASM2232146v1_genomic.fna.gz --refList GCF_022321465.1_ASM2232146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022321465.1_ASM2232146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:57,306] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:57,315] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:12:57,315] [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_000011965.2	s__Ruegeria_B pomeroyi	91.2967	1190	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_010500245.1	s__Ruegeria_B sp010500245	86.7796	1103	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	84.3176	991	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	81.2467	773	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	81.2234	763	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	81.1218	862	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	81.0428	716	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900109035.1	s__Cribrihabitans marinus	80.9538	782	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938215.1	s__Ruegeria sediminis	80.9344	767	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	80.1726	466	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.5768	608	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363615.1	s__Ruegeria sp009363615	79.288	582	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.2293	422	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	79.1119	599	1447	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:57,316] [INFO] GTDB search result was written to GCF_022321465.1_ASM2232146v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:57,317] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:57,319] [INFO] DFAST_QC result json was written to GCF_022321465.1_ASM2232146v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:57,320] [INFO] DFAST_QC completed!
[2024-01-25 18:12:57,320] [INFO] Total running time: 0h1m22s