[2024-01-24 13:28:01,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference
[2024-01-24 13:28:03,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,141] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b7be9e1-8848-434b-a109-a5e4f8f14908/GCF_021233055.1_ASM2123305v1_genomic.fna.gz | prodigal -d GCF_021233055.1_ASM2123305v1_genomic.fna/cds.fna -a GCF_021233055.1_ASM2123305v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,086] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,087] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,087] [INFO] Running command: hmmsearch --tblout GCF_021233055.1_ASM2123305v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference/reference_markers.hmm GCF_021233055.1_ASM2123305v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,406] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,473] [INFO] Query marker FASTA was written to GCF_021233055.1_ASM2123305v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,473] [INFO] Task started: Blastn
[2024-01-24 13:28:41,473] [INFO] Running command: blastn -query GCF_021233055.1_ASM2123305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference/reference_markers.fasta -out GCF_021233055.1_ASM2123305v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,056] [INFO] Selected 21 target genomes.
[2024-01-24 13:28:42,056] [INFO] Target genome list was writen to GCF_021233055.1_ASM2123305v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,094] [INFO] Task started: fastANI
[2024-01-24 13:28:42,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7be9e1-8848-434b-a109-a5e4f8f14908/GCF_021233055.1_ASM2123305v1_genomic.fna.gz --refList GCF_021233055.1_ASM2123305v1_genomic.fna/target_genomes.txt --output GCF_021233055.1_ASM2123305v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:08,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:08,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:08,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:08,107] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:29:08,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:29:08,107] [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 agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	78.6811	867	2440	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	78.6048	850	2440	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	78.5163	848	2440	95	below_threshold
Spirosoma terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	77.9679	601	2440	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.494	463	2440	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.4724	472	2440	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	77.3511	405	2440	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	77.2823	490	2440	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.2343	404	2440	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.1665	411	2440	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.1216	463	2440	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.0628	414	2440	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	77.0385	386	2440	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.0301	436	2440	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	76.9006	447	2440	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	76.1132	164	2440	95	below_threshold
Siphonobacter curvatus	strain=HR-U	GCA_002943425.1	2094562	2094562	type	True	75.616	91	2440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:08,109] [INFO] DFAST Taxonomy check result was written to GCF_021233055.1_ASM2123305v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:08,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:08,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:08,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference/checkm_data
[2024-01-24 13:29:08,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:08,177] [INFO] Task started: CheckM
[2024-01-24 13:29:08,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021233055.1_ASM2123305v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021233055.1_ASM2123305v1_genomic.fna/checkm_input GCF_021233055.1_ASM2123305v1_genomic.fna/checkm_result
[2024-01-24 13:30:43,945] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:43,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:43,968] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:43,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:43,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021233055.1_ASM2123305v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:43,969] [INFO] Task started: Blastn
[2024-01-24 13:30:43,969] [INFO] Running command: blastn -query GCF_021233055.1_ASM2123305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26fc581c-3ed2-42fd-af42-029a75e289c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_021233055.1_ASM2123305v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:44,803] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:44,806] [INFO] Selected 19 target genomes.
[2024-01-24 13:30:44,807] [INFO] Target genome list was writen to GCF_021233055.1_ASM2123305v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:44,829] [INFO] Task started: fastANI
[2024-01-24 13:30:44,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7be9e1-8848-434b-a109-a5e4f8f14908/GCF_021233055.1_ASM2123305v1_genomic.fna.gz --refList GCF_021233055.1_ASM2123305v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021233055.1_ASM2123305v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:09,003] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:09,017] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:31:09,018] [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_010747415.1	s__Spirosoma agri	78.6861	866	2440	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	78.589	848	2440	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	78.5098	850	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010435915.1	s__Spirosoma terrae	77.9734	600	2440	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	77.5994	515	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	77.5002	462	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002825.1	s__Spirosoma oryzae	77.3438	406	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	77.3247	439	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112365.1	s__Spirosoma endophyticum	77.2818	491	2440	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	77.2648	412	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002056795.1	s__Spirosoma aerolatum	77.264	404	2440	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	77.1665	411	2440	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	77.1259	412	2440	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	77.1166	464	2440	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	77.0628	414	2440	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	77.0385	386	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.0244	437	2440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_000374025.1	s__Spirosoma panaciterrae	76.9178	447	2440	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 13:31:09,019] [INFO] GTDB search result was written to GCF_021233055.1_ASM2123305v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:09,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:09,025] [INFO] DFAST_QC result json was written to GCF_021233055.1_ASM2123305v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:09,025] [INFO] DFAST_QC completed!
[2024-01-24 13:31:09,025] [INFO] Total running time: 0h3m7s