[2024-01-24 13:40:27,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:27,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:27,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference
[2024-01-24 13:40:29,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,025] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,025] [INFO] Running command: gunzip -c /var/lib/cwl/stge13310e4-cf63-49d3-bac7-e40d5c4a45e3/GCF_013372145.1_ASM1337214v1_genomic.fna.gz | prodigal -d GCF_013372145.1_ASM1337214v1_genomic.fna/cds.fna -a GCF_013372145.1_ASM1337214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:32,193] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:32,193] [INFO] Task started: HMMsearch
[2024-01-24 13:40:32,194] [INFO] Running command: hmmsearch --tblout GCF_013372145.1_ASM1337214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference/reference_markers.hmm GCF_013372145.1_ASM1337214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:32,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:32,459] [INFO] Found 6/6 markers.
[2024-01-24 13:40:32,486] [INFO] Query marker FASTA was written to GCF_013372145.1_ASM1337214v1_genomic.fna/markers.fasta
[2024-01-24 13:40:32,486] [INFO] Task started: Blastn
[2024-01-24 13:40:32,487] [INFO] Running command: blastn -query GCF_013372145.1_ASM1337214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference/reference_markers.fasta -out GCF_013372145.1_ASM1337214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:33,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:33,099] [INFO] Selected 6 target genomes.
[2024-01-24 13:40:33,099] [INFO] Target genome list was writen to GCF_013372145.1_ASM1337214v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:33,109] [INFO] Task started: fastANI
[2024-01-24 13:40:33,109] [INFO] Running command: fastANI --query /var/lib/cwl/stge13310e4-cf63-49d3-bac7-e40d5c4a45e3/GCF_013372145.1_ASM1337214v1_genomic.fna.gz --refList GCF_013372145.1_ASM1337214v1_genomic.fna/target_genomes.txt --output GCF_013372145.1_ASM1337214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:35,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:35,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:35,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:35,707] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:40:35,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:35,707] [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 hyointestinalis subsp. hyointestinalis	strain=CCUG 14169	GCA_013372145.1	91352	198	type	True	100.0	583	584	95	conclusive
Campylobacter hyointestinalis	strain=NCTC11608	GCA_900460765.1	198	198	type	True	99.9982	582	584	95	conclusive
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	99.9601	565	584	95	conclusive
Campylobacter hyointestinalis	strain=ATCC 35217	GCA_900116585.1	198	198	type	True	99.9551	573	584	95	conclusive
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	94.6718	472	584	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	94.5488	451	584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:35,709] [INFO] DFAST Taxonomy check result was written to GCF_013372145.1_ASM1337214v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:35,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:35,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:35,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference/checkm_data
[2024-01-24 13:40:35,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:35,730] [INFO] Task started: CheckM
[2024-01-24 13:40:35,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013372145.1_ASM1337214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013372145.1_ASM1337214v1_genomic.fna/checkm_input GCF_013372145.1_ASM1337214v1_genomic.fna/checkm_result
[2024-01-24 13:40:54,192] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:54,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:54,216] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:54,216] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:54,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013372145.1_ASM1337214v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:54,217] [INFO] Task started: Blastn
[2024-01-24 13:40:54,217] [INFO] Running command: blastn -query GCF_013372145.1_ASM1337214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d34e8cf-5549-4186-b645-adeee5effc15/dqc_reference/reference_markers_gtdb.fasta -out GCF_013372145.1_ASM1337214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,028] [INFO] Selected 10 target genomes.
[2024-01-24 13:40:55,028] [INFO] Target genome list was writen to GCF_013372145.1_ASM1337214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:55,047] [INFO] Task started: fastANI
[2024-01-24 13:40:55,047] [INFO] Running command: fastANI --query /var/lib/cwl/stge13310e4-cf63-49d3-bac7-e40d5c4a45e3/GCF_013372145.1_ASM1337214v1_genomic.fna.gz --refList GCF_013372145.1_ASM1337214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013372145.1_ASM1337214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:59,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:59,049] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:59,050] [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_013372145.1	s__Campylobacter hyointestinalis	100.0	583	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.64	97.83	0.93	0.88	41	conclusive
GCF_013372165.1	s__Campylobacter lawsonii	94.7143	478	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
GCA_000495505.1	s__Campylobacter testudinum	83.9344	378	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_900475935.1	s__Campylobacter fetus	82.5223	344	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_000736415.1	s__Campylobacter iguaniorum	79.8423	317	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.53	97.69	0.92	0.91	3	-
GCF_002139855.1	s__Campylobacter sp002139855	79.6301	176	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.28	98.16	0.95	0.94	4	-
GCF_002021925.1	s__Campylobacter_A pinnipediorum	77.3363	85	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	98.45	97.81	0.98	0.95	8	-
GCA_017646085.1	s__Campylobacter sp017646085	77.2244	128	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690845.1	s__Campylobacter_B portucalensis	76.3886	83	584	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:59,051] [INFO] GTDB search result was written to GCF_013372145.1_ASM1337214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:59,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:59,055] [INFO] DFAST_QC result json was written to GCF_013372145.1_ASM1337214v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:59,055] [INFO] DFAST_QC completed!
[2024-01-24 13:40:59,055] [INFO] Total running time: 0h0m31s