[2024-01-25 20:22:50,517] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference
[2024-01-25 20:22:51,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,720] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg546de2e7-0d2d-4e6e-b570-3d66ca139320/GCF_009754945.1_ASM975494v1_genomic.fna.gz | prodigal -d GCF_009754945.1_ASM975494v1_genomic.fna/cds.fna -a GCF_009754945.1_ASM975494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:26,921] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:26,921] [INFO] Task started: HMMsearch
[2024-01-25 20:23:26,921] [INFO] Running command: hmmsearch --tblout GCF_009754945.1_ASM975494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference/reference_markers.hmm GCF_009754945.1_ASM975494v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:27,327] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:27,328] [INFO] Found 6/6 markers.
[2024-01-25 20:23:27,399] [INFO] Query marker FASTA was written to GCF_009754945.1_ASM975494v1_genomic.fna/markers.fasta
[2024-01-25 20:23:27,399] [INFO] Task started: Blastn
[2024-01-25 20:23:27,399] [INFO] Running command: blastn -query GCF_009754945.1_ASM975494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference/reference_markers.fasta -out GCF_009754945.1_ASM975494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:27,957] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:27,960] [INFO] Selected 18 target genomes.
[2024-01-25 20:23:27,960] [INFO] Target genome list was writen to GCF_009754945.1_ASM975494v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:27,975] [INFO] Task started: fastANI
[2024-01-25 20:23:27,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg546de2e7-0d2d-4e6e-b570-3d66ca139320/GCF_009754945.1_ASM975494v1_genomic.fna.gz --refList GCF_009754945.1_ASM975494v1_genomic.fna/target_genomes.txt --output GCF_009754945.1_ASM975494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:55,113] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:55,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:55,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:55,124] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:55,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:55,124] [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 arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	100.0	3214	3220	95	conclusive
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	78.1733	805	3220	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	78.0819	767	3220	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	78.0531	721	3220	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.843	643	3220	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.8331	635	3220	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.8299	706	3220	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.7142	711	3220	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.6882	668	3220	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.6168	708	3220	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.5381	636	3220	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.2802	364	3220	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.1758	316	3220	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.1255	311	3220	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	76.9331	327	3220	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.0606	204	3220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:55,125] [INFO] DFAST Taxonomy check result was written to GCF_009754945.1_ASM975494v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:55,126] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:55,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:55,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference/checkm_data
[2024-01-25 20:23:55,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:55,214] [INFO] Task started: CheckM
[2024-01-25 20:23:55,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009754945.1_ASM975494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009754945.1_ASM975494v1_genomic.fna/checkm_input GCF_009754945.1_ASM975494v1_genomic.fna/checkm_result
[2024-01-25 20:25:29,040] [INFO] Task succeeded: CheckM
[2024-01-25 20:25:29,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:25:29,071] [INFO] ===== Completeness check finished =====
[2024-01-25 20:25:29,071] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:25:29,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009754945.1_ASM975494v1_genomic.fna/markers.fasta)
[2024-01-25 20:25:29,072] [INFO] Task started: Blastn
[2024-01-25 20:25:29,072] [INFO] Running command: blastn -query GCF_009754945.1_ASM975494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ce10ca7-0588-49c1-8811-2f1ed579e278/dqc_reference/reference_markers_gtdb.fasta -out GCF_009754945.1_ASM975494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:29,963] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:29,965] [INFO] Selected 14 target genomes.
[2024-01-25 20:25:29,965] [INFO] Target genome list was writen to GCF_009754945.1_ASM975494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:25:30,005] [INFO] Task started: fastANI
[2024-01-25 20:25:30,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg546de2e7-0d2d-4e6e-b570-3d66ca139320/GCF_009754945.1_ASM975494v1_genomic.fna.gz --refList GCF_009754945.1_ASM975494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009754945.1_ASM975494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:53,341] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:53,350] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:53,350] [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_009754945.1	s__Spirosoma sp009754945	100.0	3214	3220	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_014117325.1	s__Spirosoma sp014117325	81.657	1768	3220	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	81.5626	1748	3220	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006965485.1	s__Spirosoma sp006965485	80.9803	1607	3220	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	78.1659	806	3220	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831565.1	s__Spirosoma pollinicola	78.0736	768	3220	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	77.9053	681	3220	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	77.833	635	3220	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	77.7093	712	3220	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699035.1	s__Spirosoma validum	77.6773	671	3220	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	77.6134	708	3220	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	77.5379	636	3220	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	77.4875	488	3220	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374085.1	s__Spirosoma spitsbergense	77.4393	549	3220	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 20:25:53,351] [INFO] GTDB search result was written to GCF_009754945.1_ASM975494v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:53,352] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:53,355] [INFO] DFAST_QC result json was written to GCF_009754945.1_ASM975494v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:53,355] [INFO] DFAST_QC completed!
[2024-01-25 20:25:53,355] [INFO] Total running time: 0h3m3s