[2024-01-25 19:08:35,575] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:35,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:35,577] [INFO] DQC Reference Directory: /var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference
[2024-01-25 19:08:36,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:36,746] [INFO] Task started: Prodigal
[2024-01-25 19:08:36,746] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5ac43b9-8905-4ff3-ad50-8cc1742561b9/GCF_000374085.1_ASM37408v1_genomic.fna.gz | prodigal -d GCF_000374085.1_ASM37408v1_genomic.fna/cds.fna -a GCF_000374085.1_ASM37408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:05,339] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:05,339] [INFO] Task started: HMMsearch
[2024-01-25 19:09:05,340] [INFO] Running command: hmmsearch --tblout GCF_000374085.1_ASM37408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference/reference_markers.hmm GCF_000374085.1_ASM37408v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:05,671] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:05,672] [INFO] Found 6/6 markers.
[2024-01-25 19:09:05,729] [INFO] Query marker FASTA was written to GCF_000374085.1_ASM37408v1_genomic.fna/markers.fasta
[2024-01-25 19:09:05,729] [INFO] Task started: Blastn
[2024-01-25 19:09:05,729] [INFO] Running command: blastn -query GCF_000374085.1_ASM37408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference/reference_markers.fasta -out GCF_000374085.1_ASM37408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:06,291] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:06,294] [INFO] Selected 16 target genomes.
[2024-01-25 19:09:06,295] [INFO] Target genome list was writen to GCF_000374085.1_ASM37408v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:06,307] [INFO] Task started: fastANI
[2024-01-25 19:09:06,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ac43b9-8905-4ff3-ad50-8cc1742561b9/GCF_000374085.1_ASM37408v1_genomic.fna.gz --refList GCF_000374085.1_ASM37408v1_genomic.fna/target_genomes.txt --output GCF_000374085.1_ASM37408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:27,061] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:27,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:27,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:27,071] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:27,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:27,071] [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 spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	100.0	2378	2389	95	conclusive
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	86.2729	1622	2389	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	77.5278	502	2389	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.3969	520	2389	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.2702	423	2389	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.2488	520	2389	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.118	481	2389	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.1164	490	2389	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.0644	441	2389	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.0108	435	2389	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	76.9695	412	2389	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.8832	415	2389	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	76.8309	415	2389	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	76.7125	386	2389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:27,072] [INFO] DFAST Taxonomy check result was written to GCF_000374085.1_ASM37408v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:27,073] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:27,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:27,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference/checkm_data
[2024-01-25 19:09:27,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:27,143] [INFO] Task started: CheckM
[2024-01-25 19:09:27,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374085.1_ASM37408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374085.1_ASM37408v1_genomic.fna/checkm_input GCF_000374085.1_ASM37408v1_genomic.fna/checkm_result
[2024-01-25 19:10:44,118] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:44,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:44,141] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:44,142] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:44,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374085.1_ASM37408v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:44,143] [INFO] Task started: Blastn
[2024-01-25 19:10:44,143] [INFO] Running command: blastn -query GCF_000374085.1_ASM37408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4c13fb7-c6e0-46d3-b0f5-70a7422a3ffe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374085.1_ASM37408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:44,891] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:44,894] [INFO] Selected 17 target genomes.
[2024-01-25 19:10:44,894] [INFO] Target genome list was writen to GCF_000374085.1_ASM37408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:44,911] [INFO] Task started: fastANI
[2024-01-25 19:10:44,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ac43b9-8905-4ff3-ad50-8cc1742561b9/GCF_000374085.1_ASM37408v1_genomic.fna.gz --refList GCF_000374085.1_ASM37408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374085.1_ASM37408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:11,254] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:11,269] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:11,270] [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_000374085.1	s__Spirosoma spitsbergense	100.0	2378	2389	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_000374065.1	s__Spirosoma luteum	86.277	1621	2389	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	77.5969	612	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112365.1	s__Spirosoma endophyticum	77.5288	501	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000024525.1	s__Spirosoma linguale	77.5064	608	2389	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	77.3969	520	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117325.1	s__Spirosoma sp014117325	77.372	541	2389	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	77.2434	521	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898575.1	s__Spirosoma sp001898575	77.1773	500	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014699035.1	s__Spirosoma validum	77.1299	478	2389	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	77.1156	490	2389	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	77.0815	438	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	76.9749	411	2389	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	76.8832	415	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	76.8306	415	2389	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	76.7037	385	2389	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:11,278] [INFO] GTDB search result was written to GCF_000374085.1_ASM37408v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:11,279] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:11,282] [INFO] DFAST_QC result json was written to GCF_000374085.1_ASM37408v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:11,282] [INFO] DFAST_QC completed!
[2024-01-25 19:11:11,283] [INFO] Total running time: 0h2m36s