[2024-01-24 13:02:03,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,993] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference
[2024-01-24 13:02:05,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,275] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgff048382-bf0d-4dc8-a38e-1fb635d73e82/GCF_006165035.1_ASM616503v1_genomic.fna.gz | prodigal -d GCF_006165035.1_ASM616503v1_genomic.fna/cds.fna -a GCF_006165035.1_ASM616503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:08,794] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:08,795] [INFO] Task started: HMMsearch
[2024-01-24 13:02:08,795] [INFO] Running command: hmmsearch --tblout GCF_006165035.1_ASM616503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference/reference_markers.hmm GCF_006165035.1_ASM616503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:08,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:08,982] [INFO] Found 6/6 markers.
[2024-01-24 13:02:09,004] [INFO] Query marker FASTA was written to GCF_006165035.1_ASM616503v1_genomic.fna/markers.fasta
[2024-01-24 13:02:09,005] [INFO] Task started: Blastn
[2024-01-24 13:02:09,005] [INFO] Running command: blastn -query GCF_006165035.1_ASM616503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference/reference_markers.fasta -out GCF_006165035.1_ASM616503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:09,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:09,691] [INFO] Selected 10 target genomes.
[2024-01-24 13:02:09,691] [INFO] Target genome list was writen to GCF_006165035.1_ASM616503v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:09,714] [INFO] Task started: fastANI
[2024-01-24 13:02:09,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgff048382-bf0d-4dc8-a38e-1fb635d73e82/GCF_006165035.1_ASM616503v1_genomic.fna.gz --refList GCF_006165035.1_ASM616503v1_genomic.fna/target_genomes.txt --output GCF_006165035.1_ASM616503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:14,972] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:14,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:14,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:14,983] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:02:14,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:14,984] [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
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	100.0	700	701	95	conclusive
Aliarcobacter cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	99.9803	697	701	95	conclusive
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	99.8839	650	701	95	conclusive
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	86.6466	515	701	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	86.5427	498	701	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	84.8742	456	701	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	84.8096	469	701	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	83.7599	480	701	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	83.3408	447	701	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	83.3226	454	701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:14,987] [INFO] DFAST Taxonomy check result was written to GCF_006165035.1_ASM616503v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:14,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:14,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:14,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference/checkm_data
[2024-01-24 13:02:14,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:15,017] [INFO] Task started: CheckM
[2024-01-24 13:02:15,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006165035.1_ASM616503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006165035.1_ASM616503v1_genomic.fna/checkm_input GCF_006165035.1_ASM616503v1_genomic.fna/checkm_result
[2024-01-24 13:02:31,679] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:31,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:31,701] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:31,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:31,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006165035.1_ASM616503v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:31,702] [INFO] Task started: Blastn
[2024-01-24 13:02:31,702] [INFO] Running command: blastn -query GCF_006165035.1_ASM616503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6b5c19-fb47-4f2e-8623-cbfe92a15179/dqc_reference/reference_markers_gtdb.fasta -out GCF_006165035.1_ASM616503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:32,647] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:32,650] [INFO] Selected 11 target genomes.
[2024-01-24 13:02:32,650] [INFO] Target genome list was writen to GCF_006165035.1_ASM616503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:32,655] [INFO] Task started: fastANI
[2024-01-24 13:02:32,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgff048382-bf0d-4dc8-a38e-1fb635d73e82/GCF_006165035.1_ASM616503v1_genomic.fna.gz --refList GCF_006165035.1_ASM616503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006165035.1_ASM616503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:38,177] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:38,187] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:38,188] [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_003660105.1	s__Aliarcobacter cryaerophilus	99.9803	697	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	94.025	554	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCA_017996075.1	s__Aliarcobacter sp017996075	93.2572	226	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	92.8729	573	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_003355515.1	s__Aliarcobacter trophiarum	86.6652	514	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_003544835.1	s__Aliarcobacter skirrowii	85.0715	475	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_013201705.1	s__Aliarcobacter faecis	83.9643	480	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_016106035.1	s__Aliarcobacter sp016106035	83.3662	451	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004299785.2	s__Aliarcobacter porcinus	82.4968	427	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_004214815.1	s__Aliarcobacter thereius	82.3404	434	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCA_017995775.1	s__Aliarcobacter sp017995775	79.9552	348	701	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:38,189] [INFO] GTDB search result was written to GCF_006165035.1_ASM616503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:38,190] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:38,193] [INFO] DFAST_QC result json was written to GCF_006165035.1_ASM616503v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:38,193] [INFO] DFAST_QC completed!
[2024-01-24 13:02:38,193] [INFO] Total running time: 0h0m34s