[2024-01-24 13:12:37,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:37,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:37,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference
[2024-01-24 13:12:38,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:38,628] [INFO] Task started: Prodigal
[2024-01-24 13:12:38,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg333031a1-252d-4b18-bc5a-59620c47a6e8/GCF_014699005.1_ASM1469900v1_genomic.fna.gz | prodigal -d GCF_014699005.1_ASM1469900v1_genomic.fna/cds.fna -a GCF_014699005.1_ASM1469900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:18,939] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:18,940] [INFO] Task started: HMMsearch
[2024-01-24 13:13:18,940] [INFO] Running command: hmmsearch --tblout GCF_014699005.1_ASM1469900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference/reference_markers.hmm GCF_014699005.1_ASM1469900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:19,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:19,362] [INFO] Found 6/6 markers.
[2024-01-24 13:13:19,461] [INFO] Query marker FASTA was written to GCF_014699005.1_ASM1469900v1_genomic.fna/markers.fasta
[2024-01-24 13:13:19,461] [INFO] Task started: Blastn
[2024-01-24 13:13:19,461] [INFO] Running command: blastn -query GCF_014699005.1_ASM1469900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference/reference_markers.fasta -out GCF_014699005.1_ASM1469900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:20,125] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:20,128] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:20,129] [INFO] Target genome list was writen to GCF_014699005.1_ASM1469900v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:20,140] [INFO] Task started: fastANI
[2024-01-24 13:13:20,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg333031a1-252d-4b18-bc5a-59620c47a6e8/GCF_014699005.1_ASM1469900v1_genomic.fna.gz --refList GCF_014699005.1_ASM1469900v1_genomic.fna/target_genomes.txt --output GCF_014699005.1_ASM1469900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:45,562] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:45,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:45,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:45,575] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:45,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:45,575] [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 profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	100.0	2864	2868	95	conclusive
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.9346	722	2868	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.5681	646	2868	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.5346	644	2868	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.5092	530	2868	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	77.5066	612	2868	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.4985	592	2868	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.3293	529	2868	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.2304	405	2868	95	below_threshold
Spirosoma spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	77.0534	460	2868	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.0252	442	2868	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.0136	423	2868	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	76.9977	362	2868	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.9252	343	2868	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	76.2738	258	2868	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:45,577] [INFO] DFAST Taxonomy check result was written to GCF_014699005.1_ASM1469900v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:45,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:45,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:45,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference/checkm_data
[2024-01-24 13:13:45,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:45,656] [INFO] Task started: CheckM
[2024-01-24 13:13:45,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014699005.1_ASM1469900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014699005.1_ASM1469900v1_genomic.fna/checkm_input GCF_014699005.1_ASM1469900v1_genomic.fna/checkm_result
[2024-01-24 13:15:30,626] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:30,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:30,650] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:30,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:30,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014699005.1_ASM1469900v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:30,651] [INFO] Task started: Blastn
[2024-01-24 13:15:30,651] [INFO] Running command: blastn -query GCF_014699005.1_ASM1469900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg299c11be-3446-49bf-ba8c-9b978bc9a697/dqc_reference/reference_markers_gtdb.fasta -out GCF_014699005.1_ASM1469900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:31,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:31,483] [INFO] Selected 21 target genomes.
[2024-01-24 13:15:31,483] [INFO] Target genome list was writen to GCF_014699005.1_ASM1469900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:31,499] [INFO] Task started: fastANI
[2024-01-24 13:15:31,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg333031a1-252d-4b18-bc5a-59620c47a6e8/GCF_014699005.1_ASM1469900v1_genomic.fna.gz --refList GCF_014699005.1_ASM1469900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014699005.1_ASM1469900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:02,614] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:02,630] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:02,630] [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_014699005.1	s__Spirosoma profusum	100.0	2864	2868	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_014699035.1	s__Spirosoma validum	77.9342	722	2868	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	77.586	534	2868	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	77.5628	635	2868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002056795.1	s__Spirosoma aerolatum	77.5618	648	2868	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	77.5383	644	2868	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	77.5197	611	2868	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	77.4989	615	2868	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	77.4889	594	2868	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	77.4872	533	2868	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	77.4345	609	2868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011604685.1	s__Spirosoma aureum	77.2754	518	2868	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	77.2304	405	2868	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	77.0249	442	2868	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	77.0235	422	2868	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	76.9905	363	2868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_005870035.1	s__Spirosoma lacussanchae	76.9252	343	2868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	76.2667	259	2868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292855.1	s__Rudanella sp004292855	75.8095	185	2868	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	98.31	98.31	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:16:02,632] [INFO] GTDB search result was written to GCF_014699005.1_ASM1469900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:02,633] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:02,637] [INFO] DFAST_QC result json was written to GCF_014699005.1_ASM1469900v1_genomic.fna/dqc_result.json
[2024-01-24 13:16:02,637] [INFO] DFAST_QC completed!
[2024-01-24 13:16:02,637] [INFO] Total running time: 0h3m25s