[2024-01-24 14:06:59,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:59,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:59,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference
[2024-01-24 14:07:01,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:01,294] [INFO] Task started: Prodigal
[2024-01-24 14:07:01,294] [INFO] Running command: gunzip -c /var/lib/cwl/stga11ac7ee-8ca9-4e60-a817-46e4a3f9c51b/GCF_002056795.1_ASM205679v1_genomic.fna.gz | prodigal -d GCF_002056795.1_ASM205679v1_genomic.fna/cds.fna -a GCF_002056795.1_ASM205679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:37,230] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:37,230] [INFO] Task started: HMMsearch
[2024-01-24 14:07:37,230] [INFO] Running command: hmmsearch --tblout GCF_002056795.1_ASM205679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference/reference_markers.hmm GCF_002056795.1_ASM205679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:37,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:37,526] [INFO] Found 6/6 markers.
[2024-01-24 14:07:37,587] [INFO] Query marker FASTA was written to GCF_002056795.1_ASM205679v1_genomic.fna/markers.fasta
[2024-01-24 14:07:37,588] [INFO] Task started: Blastn
[2024-01-24 14:07:37,588] [INFO] Running command: blastn -query GCF_002056795.1_ASM205679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference/reference_markers.fasta -out GCF_002056795.1_ASM205679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:38,154] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:38,157] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:38,158] [INFO] Target genome list was writen to GCF_002056795.1_ASM205679v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:38,167] [INFO] Task started: fastANI
[2024-01-24 14:07:38,167] [INFO] Running command: fastANI --query /var/lib/cwl/stga11ac7ee-8ca9-4e60-a817-46e4a3f9c51b/GCF_002056795.1_ASM205679v1_genomic.fna.gz --refList GCF_002056795.1_ASM205679v1_genomic.fna/target_genomes.txt --output GCF_002056795.1_ASM205679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:03,063] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:03,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:03,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:03,077] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:03,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:03,077] [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 aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	100.0	2652	2653	95	conclusive
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	84.3217	2008	2653	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.6682	738	2653	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.6569	589	2653	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.6335	646	2653	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.4827	403	2653	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.3931	558	2653	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.3777	482	2653	95	below_threshold
Spirosoma terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	77.0951	484	2653	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.0875	342	2653	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.069	440	2653	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	77.0633	285	2653	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.0073	404	2653	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.9842	369	2653	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.1276	245	2653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:03,079] [INFO] DFAST Taxonomy check result was written to GCF_002056795.1_ASM205679v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:03,079] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:03,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:03,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference/checkm_data
[2024-01-24 14:08:03,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:03,152] [INFO] Task started: CheckM
[2024-01-24 14:08:03,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002056795.1_ASM205679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002056795.1_ASM205679v1_genomic.fna/checkm_input GCF_002056795.1_ASM205679v1_genomic.fna/checkm_result
[2024-01-24 14:09:40,175] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:40,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:40,200] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:40,200] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:40,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002056795.1_ASM205679v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:40,201] [INFO] Task started: Blastn
[2024-01-24 14:09:40,201] [INFO] Running command: blastn -query GCF_002056795.1_ASM205679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc60f8de2-ad66-4933-ab15-ef561dfdcb23/dqc_reference/reference_markers_gtdb.fasta -out GCF_002056795.1_ASM205679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:41,026] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:41,029] [INFO] Selected 15 target genomes.
[2024-01-24 14:09:41,029] [INFO] Target genome list was writen to GCF_002056795.1_ASM205679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:41,039] [INFO] Task started: fastANI
[2024-01-24 14:09:41,039] [INFO] Running command: fastANI --query /var/lib/cwl/stga11ac7ee-8ca9-4e60-a817-46e4a3f9c51b/GCF_002056795.1_ASM205679v1_genomic.fna.gz --refList GCF_002056795.1_ASM205679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002056795.1_ASM205679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:04,889] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:04,902] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:04,902] [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_002056795.1	s__Spirosoma aerolatum	100.0	2652	2653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001898575.1	s__Spirosoma sp001898575	90.918	2179	2653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000374025.1	s__Spirosoma panaciterrae	84.3329	2005	2653	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	77.981	805	2653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014117325.1	s__Spirosoma sp014117325	77.8784	743	2653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965485.1	s__Spirosoma sp006965485	77.8072	743	2653	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	77.685	734	2653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	77.656	590	2653	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	77.6395	644	2653	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	77.4438	399	2653	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	77.4035	556	2653	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	77.3779	482	2653	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	77.1108	482	2653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	77.0948	341	2653	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	77.0689	440	2653	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 14:10:04,903] [INFO] GTDB search result was written to GCF_002056795.1_ASM205679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:04,904] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:04,908] [INFO] DFAST_QC result json was written to GCF_002056795.1_ASM205679v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:04,908] [INFO] DFAST_QC completed!
[2024-01-24 14:10:04,908] [INFO] Total running time: 0h3m5s