[2024-01-24 13:49:19,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference
[2024-01-24 13:49:20,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,508] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ff9a46e-5dda-4b0b-b106-8abf4a887b1f/GCF_008271385.1_ASM827138v1_genomic.fna.gz | prodigal -d GCF_008271385.1_ASM827138v1_genomic.fna/cds.fna -a GCF_008271385.1_ASM827138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,858] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,858] [INFO] Running command: hmmsearch --tblout GCF_008271385.1_ASM827138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference/reference_markers.hmm GCF_008271385.1_ASM827138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:24,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:24,127] [INFO] Found 6/6 markers.
[2024-01-24 13:49:24,153] [INFO] Query marker FASTA was written to GCF_008271385.1_ASM827138v1_genomic.fna/markers.fasta
[2024-01-24 13:49:24,153] [INFO] Task started: Blastn
[2024-01-24 13:49:24,153] [INFO] Running command: blastn -query GCF_008271385.1_ASM827138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference/reference_markers.fasta -out GCF_008271385.1_ASM827138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:24,786] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:24,789] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:24,789] [INFO] Target genome list was writen to GCF_008271385.1_ASM827138v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:24,793] [INFO] Task started: fastANI
[2024-01-24 13:49:24,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ff9a46e-5dda-4b0b-b106-8abf4a887b1f/GCF_008271385.1_ASM827138v1_genomic.fna.gz --refList GCF_008271385.1_ASM827138v1_genomic.fna/target_genomes.txt --output GCF_008271385.1_ASM827138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:28,075] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:28,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:28,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:28,083] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:28,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:28,084] [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 fetus subsp. venerealis	strain=NCTC 10354	GCA_008271385.1	32020	196	type	True	100.0	636	637	95	conclusive
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	99.507	551	637	95	conclusive
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	99.4448	571	637	95	conclusive
Campylobacter hyointestinalis	strain=NCTC11608	GCA_900460765.1	198	198	type	True	82.6201	357	637	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	82.4423	343	637	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	82.0771	328	637	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	81.9901	338	637	95	below_threshold
Campylobacter iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	79.0635	277	637	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:28,085] [INFO] DFAST Taxonomy check result was written to GCF_008271385.1_ASM827138v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:28,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:28,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:28,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference/checkm_data
[2024-01-24 13:49:28,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:28,113] [INFO] Task started: CheckM
[2024-01-24 13:49:28,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008271385.1_ASM827138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008271385.1_ASM827138v1_genomic.fna/checkm_input GCF_008271385.1_ASM827138v1_genomic.fna/checkm_result
[2024-01-24 13:49:46,762] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:46,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,780] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:46,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:46,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008271385.1_ASM827138v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:46,781] [INFO] Task started: Blastn
[2024-01-24 13:49:46,782] [INFO] Running command: blastn -query GCF_008271385.1_ASM827138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg093df8c3-f5fb-44d3-ac82-d9be8f481c94/dqc_reference/reference_markers_gtdb.fasta -out GCF_008271385.1_ASM827138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,689] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:47,690] [INFO] Target genome list was writen to GCF_008271385.1_ASM827138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:47,696] [INFO] Task started: fastANI
[2024-01-24 13:49:47,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ff9a46e-5dda-4b0b-b106-8abf4a887b1f/GCF_008271385.1_ASM827138v1_genomic.fna.gz --refList GCF_008271385.1_ASM827138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008271385.1_ASM827138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:50,736] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:50,743] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:50,743] [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_900475935.1	s__Campylobacter fetus	99.4448	571	637	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	conclusive
GCA_000495505.1	s__Campylobacter testudinum	92.1035	555	637	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.40	99.13	0.96	0.89	37	-
GCF_013372145.1	s__Campylobacter hyointestinalis	82.6684	356	637	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.64	97.83	0.93	0.88	41	-
GCF_013372165.1	s__Campylobacter lawsonii	82.0908	350	637	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
GCF_000736415.1	s__Campylobacter iguaniorum	79.1287	279	637	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.53	97.69	0.92	0.91	3	-
GCF_013201685.1	s__Campylobacter_B geochelonis	77.0959	111	637	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.40	99.12	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,746] [INFO] GTDB search result was written to GCF_008271385.1_ASM827138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:50,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:50,749] [INFO] DFAST_QC result json was written to GCF_008271385.1_ASM827138v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:50,750] [INFO] DFAST_QC completed!
[2024-01-24 13:49:50,750] [INFO] Total running time: 0h0m32s