[2024-01-25 18:37:35,436] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:35,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:35,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference
[2024-01-25 18:37:36,589] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:36,590] [INFO] Task started: Prodigal
[2024-01-25 18:37:36,590] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ba1079e-9cbe-4705-a552-3089f3bad518/GCF_018145655.1_ASM1814565v1_genomic.fna.gz | prodigal -d GCF_018145655.1_ASM1814565v1_genomic.fna/cds.fna -a GCF_018145655.1_ASM1814565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:39,635] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:39,635] [INFO] Task started: HMMsearch
[2024-01-25 18:37:39,635] [INFO] Running command: hmmsearch --tblout GCF_018145655.1_ASM1814565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference/reference_markers.hmm GCF_018145655.1_ASM1814565v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:39,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:39,824] [INFO] Found 6/6 markers.
[2024-01-25 18:37:39,842] [INFO] Query marker FASTA was written to GCF_018145655.1_ASM1814565v1_genomic.fna/markers.fasta
[2024-01-25 18:37:39,842] [INFO] Task started: Blastn
[2024-01-25 18:37:39,843] [INFO] Running command: blastn -query GCF_018145655.1_ASM1814565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference/reference_markers.fasta -out GCF_018145655.1_ASM1814565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:40,365] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:40,368] [INFO] Selected 20 target genomes.
[2024-01-25 18:37:40,368] [INFO] Target genome list was writen to GCF_018145655.1_ASM1814565v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:40,390] [INFO] Task started: fastANI
[2024-01-25 18:37:40,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba1079e-9cbe-4705-a552-3089f3bad518/GCF_018145655.1_ASM1814565v1_genomic.fna.gz --refList GCF_018145655.1_ASM1814565v1_genomic.fna/target_genomes.txt --output GCF_018145655.1_ASM1814565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:37:47,085] [INFO] Task succeeded: fastANI
[2024-01-25 18:37:47,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:37:47,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:37:47,094] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:37:47,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:37:47,095] [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
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	100.0	605	606	95	conclusive
Campylobacter mucosalis	strain=ATCC 43264	GCA_013372205.1	202	202	type	True	78.0589	187	606	95	below_threshold
Campylobacter mucosalis	strain=ATCC 43264	GCA_012978755.1	202	202	type	True	77.9301	179	606	95	below_threshold
Campylobacter curvus	strain=FDAARGOS_1547	GCA_020736225.1	200	200	suspected-type	True	77.8649	146	606	95	below_threshold
Campylobacter curvus	strain=ATCC 35224	GCA_013372125.1	200	200	suspected-type	True	77.8428	143	606	95	below_threshold
Campylobacter curvus	strain=DSM 6644	GCA_000376325.1	200	200	suspected-type	True	77.7889	149	606	95	below_threshold
Campylobacter lanienae	strain=NCTC 13004	GCA_002139935.1	75658	75658	type	True	77.6729	62	606	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.4287	187	606	95	below_threshold
Campylobacter massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	76.9409	67	606	95	below_threshold
Campylobacter rectus	strain=FDAARGOS_1549	GCA_020736205.1	203	203	type	True	76.8648	73	606	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	76.6134	79	606	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	76.5538	94	606	95	below_threshold
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	76.5297	94	606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:37:47,097] [INFO] DFAST Taxonomy check result was written to GCF_018145655.1_ASM1814565v1_genomic.fna/tc_result.tsv
[2024-01-25 18:37:47,097] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:37:47,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:37:47,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference/checkm_data
[2024-01-25 18:37:47,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:37:47,120] [INFO] Task started: CheckM
[2024-01-25 18:37:47,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018145655.1_ASM1814565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018145655.1_ASM1814565v1_genomic.fna/checkm_input GCF_018145655.1_ASM1814565v1_genomic.fna/checkm_result
[2024-01-25 18:38:02,186] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:02,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:02,204] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:02,204] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:02,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018145655.1_ASM1814565v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:02,205] [INFO] Task started: Blastn
[2024-01-25 18:38:02,205] [INFO] Running command: blastn -query GCF_018145655.1_ASM1814565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06cc3624-9fea-4ef0-bde6-e5bb507c8237/dqc_reference/reference_markers_gtdb.fasta -out GCF_018145655.1_ASM1814565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:03,040] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:03,043] [INFO] Selected 24 target genomes.
[2024-01-25 18:38:03,043] [INFO] Target genome list was writen to GCF_018145655.1_ASM1814565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:03,066] [INFO] Task started: fastANI
[2024-01-25 18:38:03,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ba1079e-9cbe-4705-a552-3089f3bad518/GCF_018145655.1_ASM1814565v1_genomic.fna.gz --refList GCF_018145655.1_ASM1814565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018145655.1_ASM1814565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:10,927] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:10,938] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:38:10,938] [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_018145735.1	s__Campylobacter_A sp018145735	99.0481	559	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.06	99.05	0.97	0.96	3	conclusive
GCF_004803835.1	s__Campylobacter_A sp004803835	78.0687	197	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.48	98.76	0.97	0.94	10	-
GCF_002165775.1	s__Campylobacter_A concisus_E	77.7162	176	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_902460845.1	s__Campylobacter_A concisus_X	77.6807	179	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.79	99.67	0.94	0.93	3	-
GCF_902460545.1	s__Campylobacter_A concisus_AE	77.6216	187	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.012	98.08	97.56	0.95	0.93	4	-
GCF_003048615.2	s__Campylobacter_A concisus_C	77.6054	176	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	96.12	95.77	0.93	0.88	42	-
GCF_002914005.1	s__Campylobacter_A concisus_N	77.5794	168	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.90	98.90	0.94	0.94	2	-
GCF_003049085.1	s__Campylobacter_A concisus_H	77.5432	187	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.031	N/A	N/A	N/A	N/A	1	-
GCF_002139855.1	s__Campylobacter sp002139855	77.5411	65	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCF_003048675.2	s__Campylobacter_A concisus_F	77.44	185	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	95.49	95.08	0.92	0.88	22	-
GCF_004803855.2	s__Campylobacter_A sp004803855	77.4236	115	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002913945.1	s__Campylobacter_A concisus_P	77.3696	179	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003048535.1	s__Campylobacter_A concisus_S	77.3508	197	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002022005.1	s__Campylobacter_A caledonicus	77.3469	120	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.31	99.26	0.98	0.97	3	-
GCF_003048375.1	s__Campylobacter_A concisus_T	77.3356	195	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.30	95.13	0.90	0.85	33	-
GCF_002021925.1	s__Campylobacter_A pinnipediorum	77.202	123	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.45	97.81	0.98	0.95	8	-
GCF_012978815.1	s__Campylobacter_A sp012978815	77.0547	108	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	97.78	96.09	0.95	0.93	3	-
GCF_013201685.1	s__Campylobacter_B geochelonis	76.5519	93	606	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.40	99.12	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:38:10,940] [INFO] GTDB search result was written to GCF_018145655.1_ASM1814565v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:10,940] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:10,943] [INFO] DFAST_QC result json was written to GCF_018145655.1_ASM1814565v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:10,943] [INFO] DFAST_QC completed!
[2024-01-25 18:38:10,943] [INFO] Total running time: 0h0m36s