[2024-01-24 13:12:56,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference
[2024-01-24 13:12:57,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,589] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4fab11a-7ddd-4f0b-83b0-214003788248/GCF_004217095.1_ASM421709v1_genomic.fna.gz | prodigal -d GCF_004217095.1_ASM421709v1_genomic.fna/cds.fna -a GCF_004217095.1_ASM421709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:14,011] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:14,011] [INFO] Task started: HMMsearch
[2024-01-24 13:13:14,011] [INFO] Running command: hmmsearch --tblout GCF_004217095.1_ASM421709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference/reference_markers.hmm GCF_004217095.1_ASM421709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:14,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:14,316] [INFO] Found 6/6 markers.
[2024-01-24 13:13:14,363] [INFO] Query marker FASTA was written to GCF_004217095.1_ASM421709v1_genomic.fna/markers.fasta
[2024-01-24 13:13:14,363] [INFO] Task started: Blastn
[2024-01-24 13:13:14,363] [INFO] Running command: blastn -query GCF_004217095.1_ASM421709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference/reference_markers.fasta -out GCF_004217095.1_ASM421709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:15,118] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:15,122] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:15,123] [INFO] Target genome list was writen to GCF_004217095.1_ASM421709v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:15,137] [INFO] Task started: fastANI
[2024-01-24 13:13:15,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4fab11a-7ddd-4f0b-83b0-214003788248/GCF_004217095.1_ASM421709v1_genomic.fna.gz --refList GCF_004217095.1_ASM421709v1_genomic.fna/target_genomes.txt --output GCF_004217095.1_ASM421709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:31,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:31,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:31,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:31,948] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:31,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:31,948] [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
Advenella incenata	strain=DSM 23814	GCA_004217095.1	267800	267800	type	True	100.0	1632	1634	95	conclusive
Advenella kashmirensis	strain=WT001	GCA_000219915.3	310575	310575	type	True	89.9262	1297	1634	95	below_threshold
Advenella mimigardefordensis	strain=DPN7	GCA_000521505.1	302406	302406	type	True	84.3721	1168	1634	95	below_threshold
Advenella mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	77.317	161	1634	95	below_threshold
Advenella alkanexedens	strain=LAM0050	GCA_019132845.1	1481665	1481665	type	True	77.1032	141	1634	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	76.7915	113	1634	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	76.7529	112	1634	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	76.6907	105	1634	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	76.6341	103	1634	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.2602	167	1634	95	below_threshold
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	76.166	147	1634	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.0671	73	1634	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	76.0181	145	1634	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	76.0042	159	1634	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	75.9524	147	1634	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	75.5988	82	1634	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	75.443	81	1634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:31,950] [INFO] DFAST Taxonomy check result was written to GCF_004217095.1_ASM421709v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:31,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:31,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:31,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference/checkm_data
[2024-01-24 13:13:31,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:32,000] [INFO] Task started: CheckM
[2024-01-24 13:13:32,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217095.1_ASM421709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217095.1_ASM421709v1_genomic.fna/checkm_input GCF_004217095.1_ASM421709v1_genomic.fna/checkm_result
[2024-01-24 13:14:20,012] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:20,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:20,036] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:20,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:20,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217095.1_ASM421709v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:20,037] [INFO] Task started: Blastn
[2024-01-24 13:14:20,037] [INFO] Running command: blastn -query GCF_004217095.1_ASM421709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e07622f-eb46-44c7-9383-6bf1b4d90be5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217095.1_ASM421709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:21,201] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:21,205] [INFO] Selected 7 target genomes.
[2024-01-24 13:14:21,205] [INFO] Target genome list was writen to GCF_004217095.1_ASM421709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:21,221] [INFO] Task started: fastANI
[2024-01-24 13:14:21,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4fab11a-7ddd-4f0b-83b0-214003788248/GCF_004217095.1_ASM421709v1_genomic.fna.gz --refList GCF_004217095.1_ASM421709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217095.1_ASM421709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:29,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:29,324] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:29,324] [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_004217095.1	s__Advenella incenata	100.0	1632	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	99.05	99.05	0.92	0.92	2	conclusive
GCF_014897675.1	s__Advenella sp003533245	91.0584	1272	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.87	98.87	0.91	0.91	2	-
GCF_000219915.2	s__Advenella kashmirensis	89.9262	1297	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.94	98.94	0.95	0.95	2	-
GCF_000521505.1	s__Advenella mimigardefordensis	84.3732	1168	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002810445.1	s__Advenella sp002810445	83.8615	1012	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000506985.1	s__Advenella kashmirensis_A	80.644	861	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153685.1	s__Pusillimonas_C harenae	76.6907	105	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:29,326] [INFO] GTDB search result was written to GCF_004217095.1_ASM421709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:29,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:29,330] [INFO] DFAST_QC result json was written to GCF_004217095.1_ASM421709v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:29,330] [INFO] DFAST_QC completed!
[2024-01-24 13:14:29,330] [INFO] Total running time: 0h1m33s