[2024-01-24 14:15:34,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference
[2024-01-24 14:15:35,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,954] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg139fab33-d4e2-4927-8eec-521435ef4cf3/GCF_003289475.1_ASM328947v1_genomic.fna.gz | prodigal -d GCF_003289475.1_ASM328947v1_genomic.fna/cds.fna -a GCF_003289475.1_ASM328947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:39,110] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:39,111] [INFO] Task started: HMMsearch
[2024-01-24 14:15:39,111] [INFO] Running command: hmmsearch --tblout GCF_003289475.1_ASM328947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference/reference_markers.hmm GCF_003289475.1_ASM328947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:39,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:39,382] [INFO] Found 6/6 markers.
[2024-01-24 14:15:39,402] [INFO] Query marker FASTA was written to GCF_003289475.1_ASM328947v1_genomic.fna/markers.fasta
[2024-01-24 14:15:39,403] [INFO] Task started: Blastn
[2024-01-24 14:15:39,403] [INFO] Running command: blastn -query GCF_003289475.1_ASM328947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference/reference_markers.fasta -out GCF_003289475.1_ASM328947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:40,020] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:40,023] [INFO] Selected 5 target genomes.
[2024-01-24 14:15:40,024] [INFO] Target genome list was writen to GCF_003289475.1_ASM328947v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:40,030] [INFO] Task started: fastANI
[2024-01-24 14:15:40,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg139fab33-d4e2-4927-8eec-521435ef4cf3/GCF_003289475.1_ASM328947v1_genomic.fna.gz --refList GCF_003289475.1_ASM328947v1_genomic.fna/target_genomes.txt --output GCF_003289475.1_ASM328947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:42,260] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:42,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:42,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:42,267] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:15:42,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:42,267] [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. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	100.0	552	556	95	conclusive
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	99.9997	554	556	95	conclusive
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	99.9933	556	556	95	conclusive
Campylobacter hyointestinalis	strain=NCTC11608	GCA_900460765.1	198	198	type	True	94.5917	456	556	95	below_threshold
Campylobacter hyointestinalis subsp. hyointestinalis	strain=DSM 19053	GCA_000705275.1	91352	198	type	True	94.5845	445	556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:42,269] [INFO] DFAST Taxonomy check result was written to GCF_003289475.1_ASM328947v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:42,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:42,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:42,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference/checkm_data
[2024-01-24 14:15:42,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:42,291] [INFO] Task started: CheckM
[2024-01-24 14:15:42,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003289475.1_ASM328947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003289475.1_ASM328947v1_genomic.fna/checkm_input GCF_003289475.1_ASM328947v1_genomic.fna/checkm_result
[2024-01-24 14:16:00,715] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:00,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:00,737] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:00,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:00,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003289475.1_ASM328947v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:00,738] [INFO] Task started: Blastn
[2024-01-24 14:16:00,738] [INFO] Running command: blastn -query GCF_003289475.1_ASM328947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47774b1e-40a6-4e5f-96b4-20b6ebda2740/dqc_reference/reference_markers_gtdb.fasta -out GCF_003289475.1_ASM328947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:01,551] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:01,555] [INFO] Selected 12 target genomes.
[2024-01-24 14:16:01,556] [INFO] Target genome list was writen to GCF_003289475.1_ASM328947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:01,562] [INFO] Task started: fastANI
[2024-01-24 14:16:01,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg139fab33-d4e2-4927-8eec-521435ef4cf3/GCF_003289475.1_ASM328947v1_genomic.fna.gz --refList GCF_003289475.1_ASM328947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003289475.1_ASM328947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:05,972] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:05,986] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:05,986] [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_013372165.1	s__Campylobacter lawsonii	99.9933	556	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	conclusive
GCF_013372145.1	s__Campylobacter hyointestinalis	94.592	456	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.64	97.83	0.93	0.88	41	-
GCF_002139935.1	s__Campylobacter lanienae	82.5036	200	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.68	97.32	0.93	0.87	30	-
GCA_000495505.1	s__Campylobacter testudinum	82.4563	334	556	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	81.4681	315	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	-
GCF_002139855.1	s__Campylobacter sp002139855	80.3241	201	556	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	79.5123	131	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.29	97.15	0.81	0.79	3	-
GCF_000736415.1	s__Campylobacter iguaniorum	79.4289	288	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.53	97.69	0.92	0.91	3	-
GCF_002139875.1	s__Campylobacter sp002139875	79.1407	165	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.96	97.26	0.92	0.83	16	-
GCF_009690845.1	s__Campylobacter_B portucalensis	78.8464	99	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017646085.1	s__Campylobacter sp017646085	78.4064	130	556	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:05,988] [INFO] GTDB search result was written to GCF_003289475.1_ASM328947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:05,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:05,991] [INFO] DFAST_QC result json was written to GCF_003289475.1_ASM328947v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:05,991] [INFO] DFAST_QC completed!
[2024-01-24 14:16:05,991] [INFO] Total running time: 0h0m31s