[2024-01-24 14:30:45,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:45,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:45,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference
[2024-01-24 14:30:46,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,270] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,270] [INFO] Running command: gunzip -c /var/lib/cwl/stg614d1f2c-68a9-4662-a16b-e741c06bdd0b/GCF_014644035.1_ASM1464403v1_genomic.fna.gz | prodigal -d GCF_014644035.1_ASM1464403v1_genomic.fna/cds.fna -a GCF_014644035.1_ASM1464403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:57,291] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:57,291] [INFO] Task started: HMMsearch
[2024-01-24 14:30:57,291] [INFO] Running command: hmmsearch --tblout GCF_014644035.1_ASM1464403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference/reference_markers.hmm GCF_014644035.1_ASM1464403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:57,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:57,626] [INFO] Found 6/6 markers.
[2024-01-24 14:30:57,658] [INFO] Query marker FASTA was written to GCF_014644035.1_ASM1464403v1_genomic.fna/markers.fasta
[2024-01-24 14:30:57,659] [INFO] Task started: Blastn
[2024-01-24 14:30:57,659] [INFO] Running command: blastn -query GCF_014644035.1_ASM1464403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference/reference_markers.fasta -out GCF_014644035.1_ASM1464403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:58,589] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:58,600] [INFO] Selected 15 target genomes.
[2024-01-24 14:30:58,600] [INFO] Target genome list was writen to GCF_014644035.1_ASM1464403v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:58,607] [INFO] Task started: fastANI
[2024-01-24 14:30:58,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg614d1f2c-68a9-4662-a16b-e741c06bdd0b/GCF_014644035.1_ASM1464403v1_genomic.fna.gz --refList GCF_014644035.1_ASM1464403v1_genomic.fna/target_genomes.txt --output GCF_014644035.1_ASM1464403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:11,179] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:11,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:11,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:11,192] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:11,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:11,192] [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
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	100.0	1141	1141	95	conclusive
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	99.9984	1136	1141	95	conclusive
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	80.2198	572	1141	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	80.2141	506	1141	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	80.0086	583	1141	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	79.3442	470	1141	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	79.0441	437	1141	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	77.3373	242	1141	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	77.2255	225	1141	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.1552	54	1141	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	76.0965	76	1141	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.0431	53	1141	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	76.0152	72	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:11,194] [INFO] DFAST Taxonomy check result was written to GCF_014644035.1_ASM1464403v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:11,194] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:11,194] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:11,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference/checkm_data
[2024-01-24 14:31:11,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:11,231] [INFO] Task started: CheckM
[2024-01-24 14:31:11,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644035.1_ASM1464403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644035.1_ASM1464403v1_genomic.fna/checkm_input GCF_014644035.1_ASM1464403v1_genomic.fna/checkm_result
[2024-01-24 14:31:46,978] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:46,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:46,993] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:46,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:46,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644035.1_ASM1464403v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:46,994] [INFO] Task started: Blastn
[2024-01-24 14:31:46,994] [INFO] Running command: blastn -query GCF_014644035.1_ASM1464403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41b5d5b6-daab-4627-98fc-39509ebc4526/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644035.1_ASM1464403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:48,543] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:48,546] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:48,546] [INFO] Target genome list was writen to GCF_014644035.1_ASM1464403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:48,555] [INFO] Task started: fastANI
[2024-01-24 14:31:48,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg614d1f2c-68a9-4662-a16b-e741c06bdd0b/GCF_014644035.1_ASM1464403v1_genomic.fna.gz --refList GCF_014644035.1_ASM1464403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644035.1_ASM1464403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:57,645] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:57,661] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:57,661] [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_002088945.1	s__Henriciella pelagia	99.9984	1136	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003576285.1	s__Henriciella sp003576285	80.8145	566	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_002088935.1	s__Henriciella litoralis	80.2141	506	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	80.0038	582	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960415.1	s__Henriciella sp012960415	79.6244	476	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003576245.1	s__Henriciella algicola	79.3442	470	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792385.1	s__Hyphomonas sp017792385	79.2129	280	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733705.1	s__Henriciella sp002733705	79.1257	440	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_000376805.1	s__Henriciella marina	79.1099	451	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961695.1	s__Hyphomonas sp000961695	77.6712	248	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	77.2379	224	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830285.1	s__Hyphomonas sp018830285	76.9158	225	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213825.1	s__Henriciella sp013213825	75.6955	76	1141	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:57,663] [INFO] GTDB search result was written to GCF_014644035.1_ASM1464403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:57,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:57,667] [INFO] DFAST_QC result json was written to GCF_014644035.1_ASM1464403v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:57,668] [INFO] DFAST_QC completed!
[2024-01-24 14:31:57,668] [INFO] Total running time: 0h1m13s