[2024-01-25 19:37:20,410] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:20,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:20,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference
[2024-01-25 19:37:21,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:21,567] [INFO] Task started: Prodigal
[2024-01-25 19:37:21,567] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd36b184-cbe9-4fae-8431-ea10b766dfba/GCF_013201685.1_ASM1320168v1_genomic.fna.gz | prodigal -d GCF_013201685.1_ASM1320168v1_genomic.fna/cds.fna -a GCF_013201685.1_ASM1320168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:25,057] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:25,057] [INFO] Task started: HMMsearch
[2024-01-25 19:37:25,057] [INFO] Running command: hmmsearch --tblout GCF_013201685.1_ASM1320168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference/reference_markers.hmm GCF_013201685.1_ASM1320168v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:25,227] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:25,228] [INFO] Found 6/6 markers.
[2024-01-25 19:37:25,250] [INFO] Query marker FASTA was written to GCF_013201685.1_ASM1320168v1_genomic.fna/markers.fasta
[2024-01-25 19:37:25,250] [INFO] Task started: Blastn
[2024-01-25 19:37:25,250] [INFO] Running command: blastn -query GCF_013201685.1_ASM1320168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference/reference_markers.fasta -out GCF_013201685.1_ASM1320168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:25,786] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:25,790] [INFO] Selected 19 target genomes.
[2024-01-25 19:37:25,790] [INFO] Target genome list was writen to GCF_013201685.1_ASM1320168v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:25,796] [INFO] Task started: fastANI
[2024-01-25 19:37:25,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd36b184-cbe9-4fae-8431-ea10b766dfba/GCF_013201685.1_ASM1320168v1_genomic.fna.gz --refList GCF_013201685.1_ASM1320168v1_genomic.fna/target_genomes.txt --output GCF_013201685.1_ASM1320168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:31,459] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:31,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:31,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:31,470] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:37:31,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:31,470] [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 geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	100.0	717	722	95	conclusive
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	99.9261	679	722	95	conclusive
Campylobacter iguaniorum	strain=1485E	GCA_000736415.1	1244531	1244531	type	True	78.0227	119	722	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_013372165.1	91353	198	type	True	77.7131	111	722	95	below_threshold
Campylobacter fetus subsp. venerealis	strain=NCTC 10354	GCA_008271385.1	32020	196	type	True	77.6606	99	722	95	below_threshold
Campylobacter massiliensis	strain=Marseille-Q3452	GCA_014253065.1	2762557	2762557	type	True	77.5952	57	722	95	below_threshold
Campylobacter fetus subsp. fetus	strain=NCTC10842	GCA_900475935.1	32019	196	type	True	77.5713	97	722	95	below_threshold
Campylobacter blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	77.5184	167	722	95	below_threshold
Campylobacter concisus	strain=ATCC 33237	GCA_001298465.1	199	199	suspected-type	True	77.298	98	722	95	below_threshold
Campylobacter corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	77.2821	165	722	95	below_threshold
Campylobacter blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	77.2207	163	722	95	below_threshold
Campylobacter fetus subsp. fetus	strain=CCUG 6823 AT	GCA_008693125.1	32019	196	type	True	77.1887	98	722	95	below_threshold
Campylobacter corcagiensis	strain=CIT 045	GCA_000597805.1	1448857	1448857	type	True	76.9527	161	722	95	below_threshold
Campylobacter portucalensis	strain=FMV-PI01	GCA_009690845.1	2608384	2608384	type	True	76.8737	160	722	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CHY5	GCA_003289475.1	91353	198	type	True	76.7834	101	722	95	below_threshold
Campylobacter hyointestinalis subsp. lawsonii	strain=CCUG 34538	GCA_008802075.1	91353	198	type	True	76.7126	105	722	95	below_threshold
Campylobacter anatolicus	strain=faydin-G140	GCA_018145655.1	2829105	2829105	type	True	76.35	102	722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:31,472] [INFO] DFAST Taxonomy check result was written to GCF_013201685.1_ASM1320168v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:31,473] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:31,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:31,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference/checkm_data
[2024-01-25 19:37:31,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:31,497] [INFO] Task started: CheckM
[2024-01-25 19:37:31,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201685.1_ASM1320168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201685.1_ASM1320168v1_genomic.fna/checkm_input GCF_013201685.1_ASM1320168v1_genomic.fna/checkm_result
[2024-01-25 19:37:47,546] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:47,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:47,561] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:47,561] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:47,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201685.1_ASM1320168v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:47,562] [INFO] Task started: Blastn
[2024-01-25 19:37:47,562] [INFO] Running command: blastn -query GCF_013201685.1_ASM1320168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29dab91a-32bf-4522-ba6d-3d5ce7f5bbd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201685.1_ASM1320168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:48,338] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:48,341] [INFO] Selected 21 target genomes.
[2024-01-25 19:37:48,342] [INFO] Target genome list was writen to GCF_013201685.1_ASM1320168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:48,357] [INFO] Task started: fastANI
[2024-01-25 19:37:48,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd36b184-cbe9-4fae-8431-ea10b766dfba/GCF_013201685.1_ASM1320168v1_genomic.fna.gz --refList GCF_013201685.1_ASM1320168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201685.1_ASM1320168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:55,125] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:55,135] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:55,136] [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_013201685.1	s__Campylobacter_B geochelonis	100.0	718	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.40	99.12	0.97	0.95	4	conclusive
GCF_000736415.1	s__Campylobacter iguaniorum	78.192	119	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.53	97.69	0.92	0.91	3	-
GCF_000413435.1	s__Campylobacter_B ureolyticus_A	77.5803	162	722	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_000495505.1	s__Campylobacter testudinum	77.5413	115	722	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	77.5125	100	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	99.49	97.66	0.95	0.91	71	-
GCF_013201895.1	s__Campylobacter_B blaseri	77.4917	169	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013372165.1	s__Campylobacter lawsonii	77.4346	111	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	98.50	98.05	0.94	0.87	13	-
GCF_003048835.2	s__Campylobacter_A concisus_D	77.3937	95	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0092	97.26	95.33	0.94	0.89	6	-
GCF_013201645.1	s__Campylobacter_B corcagiensis	77.3172	163	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002912895.1	s__Campylobacter_A concisus_G	76.9884	91	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.40	95.36	0.91	0.89	5	-
GCA_012728225.1	s__Campylobacter_B sp012728225	76.9831	98	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001891085.1	s__Campylobacter_A concisus_O	76.9449	95	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	95.13	95.13	0.93	0.93	2	-
GCA_012519705.1	s__Campylobacter_B sp012519705	76.8857	164	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690845.1	s__Campylobacter_B portucalensis	76.8704	161	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003048535.1	s__Campylobacter_A concisus_S	76.8329	96	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469645.1	s__Campylobacter_B sp017469645	76.808	128	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	95.68	95.54	0.84	0.81	3	-
GCF_005406205.1	s__Campylobacter_D estrildidarum	76.3308	51	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017646085.1	s__Campylobacter sp017646085	76.1814	64	722	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:55,137] [INFO] GTDB search result was written to GCF_013201685.1_ASM1320168v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:55,138] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:55,141] [INFO] DFAST_QC result json was written to GCF_013201685.1_ASM1320168v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:55,141] [INFO] DFAST_QC completed!
[2024-01-25 19:37:55,141] [INFO] Total running time: 0h0m35s