[2024-01-24 13:57:30,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:30,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:30,914] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference
[2024-01-24 13:57:32,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:32,238] [INFO] Task started: Prodigal
[2024-01-24 13:57:32,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg6026637d-2ef6-431c-b5d5-8ced0142c028/GCF_000736415.1_ASM73641v1_genomic.fna.gz | prodigal -d GCF_000736415.1_ASM73641v1_genomic.fna/cds.fna -a GCF_000736415.1_ASM73641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:35,860] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:35,861] [INFO] Task started: HMMsearch
[2024-01-24 13:57:35,861] [INFO] Running command: hmmsearch --tblout GCF_000736415.1_ASM73641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference/reference_markers.hmm GCF_000736415.1_ASM73641v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:36,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:36,050] [INFO] Found 6/6 markers.
[2024-01-24 13:57:36,074] [INFO] Query marker FASTA was written to GCF_000736415.1_ASM73641v1_genomic.fna/markers.fasta
[2024-01-24 13:57:36,074] [INFO] Task started: Blastn
[2024-01-24 13:57:36,074] [INFO] Running command: blastn -query GCF_000736415.1_ASM73641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference/reference_markers.fasta -out GCF_000736415.1_ASM73641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:36,640] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:36,652] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:36,652] [INFO] Target genome list was writen to GCF_000736415.1_ASM73641v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:36,658] [INFO] Task started: fastANI
[2024-01-24 13:57:36,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg6026637d-2ef6-431c-b5d5-8ced0142c028/GCF_000736415.1_ASM73641v1_genomic.fna.gz --refList GCF_000736415.1_ASM73641v1_genomic.fna/target_genomes.txt --output GCF_000736415.1_ASM73641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:41,965] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:41,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:41,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:41,984] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:41,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:41,985] [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 iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	100.0	582	584	95	conclusive
Campylobacter hyointestinalis subsp. hyointestinalis	strain=CCUG 14169	GCA_013372145.1	91352	198	type	True	80.1225	304	584	95	below_threshold
Campylobacter hyointestinalis	strain=NCTC11608	GCA_900460765.1	198	198	type	True	80.0799	304	584	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	79.7403	299	584	95	below_threshold
Campylobacter hyointestinalis	strain=ATCC 35217	GCA_900116585.1	198	198	type	True	79.6414	319	584	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	79.3592	290	584	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	79.3339	298	584	95	below_threshold
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	79.2035	275	584	95	below_threshold
Campylobacter fetus subsp. venerealis	strain=NCTC 10354	GCA_008271385.1	32020	196	type	True	79.1168	273	584	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	78.9874	272	584	95	below_threshold
Campylobacter lanienae	strain=NCTC 13004	GCA_002139935.1	75658	75658	type	True	78.5424	161	584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:41,986] [INFO] DFAST Taxonomy check result was written to GCF_000736415.1_ASM73641v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:41,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:41,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:41,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference/checkm_data
[2024-01-24 13:57:41,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:42,010] [INFO] Task started: CheckM
[2024-01-24 13:57:42,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000736415.1_ASM73641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000736415.1_ASM73641v1_genomic.fna/checkm_input GCF_000736415.1_ASM73641v1_genomic.fna/checkm_result
[2024-01-24 13:58:00,382] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:00,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:00,404] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:00,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:00,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000736415.1_ASM73641v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:00,405] [INFO] Task started: Blastn
[2024-01-24 13:58:00,405] [INFO] Running command: blastn -query GCF_000736415.1_ASM73641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf47a36f-35f7-4774-997b-ef366d200be8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000736415.1_ASM73641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:01,165] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:01,168] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:01,168] [INFO] Target genome list was writen to GCF_000736415.1_ASM73641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:01,176] [INFO] Task started: fastANI
[2024-01-24 13:58:01,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg6026637d-2ef6-431c-b5d5-8ced0142c028/GCF_000736415.1_ASM73641v1_genomic.fna.gz --refList GCF_000736415.1_ASM73641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000736415.1_ASM73641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:05,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:05,574] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:05,575] [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_000736415.1	s__Campylobacter iguaniorum	100.0	582	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.53	97.69	0.92	0.91	3	conclusive
GCF_013372145.1	s__Campylobacter hyointestinalis	80.1084	304	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.64	97.83	0.93	0.88	41	-
GCA_000495505.1	s__Campylobacter testudinum	79.7862	284	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.40	99.13	0.96	0.89	37	-
GCF_013372165.1	s__Campylobacter lawsonii	79.6239	303	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
GCF_900475935.1	s__Campylobacter fetus	79.2166	278	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	-
GCF_002139935.1	s__Campylobacter lanienae	78.6122	160	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.68	97.32	0.93	0.87	30	-
GCF_002139875.1	s__Campylobacter sp002139875	78.4238	152	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.96	97.26	0.92	0.83	16	-
GCF_002139915.1	s__Campylobacter sp002139915	78.4057	150	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.90	97.72	0.92	0.90	37	-
GCF_002139855.1	s__Campylobacter sp002139855	78.3306	162	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCA_017506845.1	s__Campylobacter sp017506845	77.5932	120	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.29	97.15	0.81	0.79	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:05,576] [INFO] GTDB search result was written to GCF_000736415.1_ASM73641v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:05,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:05,580] [INFO] DFAST_QC result json was written to GCF_000736415.1_ASM73641v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:05,580] [INFO] DFAST_QC completed!
[2024-01-24 13:58:05,581] [INFO] Total running time: 0h0m35s