[2024-01-24 13:18:33,035] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference
[2024-01-24 13:18:34,452] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,453] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,453] [INFO] Running command: gunzip -c /var/lib/cwl/stge7c6473a-1a91-4027-b4bb-779a025659ac/GCF_013201645.1_ASM1320164v1_genomic.fna.gz | prodigal -d GCF_013201645.1_ASM1320164v1_genomic.fna/cds.fna -a GCF_013201645.1_ASM1320164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:37,401] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:37,401] [INFO] Task started: HMMsearch
[2024-01-24 13:18:37,401] [INFO] Running command: hmmsearch --tblout GCF_013201645.1_ASM1320164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference/reference_markers.hmm GCF_013201645.1_ASM1320164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:37,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:37,636] [INFO] Found 6/6 markers.
[2024-01-24 13:18:37,659] [INFO] Query marker FASTA was written to GCF_013201645.1_ASM1320164v1_genomic.fna/markers.fasta
[2024-01-24 13:18:37,659] [INFO] Task started: Blastn
[2024-01-24 13:18:37,660] [INFO] Running command: blastn -query GCF_013201645.1_ASM1320164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference/reference_markers.fasta -out GCF_013201645.1_ASM1320164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:38,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:38,331] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:38,332] [INFO] Target genome list was writen to GCF_013201645.1_ASM1320164v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:38,419] [INFO] Task started: fastANI
[2024-01-24 13:18:38,419] [INFO] Running command: fastANI --query /var/lib/cwl/stge7c6473a-1a91-4027-b4bb-779a025659ac/GCF_013201645.1_ASM1320164v1_genomic.fna.gz --refList GCF_013201645.1_ASM1320164v1_genomic.fna/target_genomes.txt --output GCF_013201645.1_ASM1320164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:43,299] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:43,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:43,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:43,313] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:43,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:43,314] [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 corcagiensis	strain=LMG 27932	GCA_013201645.1	1448857	1448857	type	True	100.0	562	563	95	conclusive
Campylobacter corcagiensis	strain=CIT 045	GCA_000597805.1	1448857	1448857	type	True	99.9637	545	563	95	conclusive
Campylobacter ureolyticus	strain=NCTC10941	GCA_900460885.1	827	827	suspected-type	True	78.2578	233	563	95	below_threshold
Campylobacter ureolyticus	strain=FDAARGOS_1102	GCA_016766895.1	827	827	suspected-type	True	78.2575	227	563	95	below_threshold
Campylobacter ureolyticus	strain=DSM 20703	GCA_000374605.1	827	827	suspected-type	True	77.9019	217	563	95	below_threshold
Campylobacter geochelonis	strain=LMG 29375	GCA_013201685.1	1780362	1780362	type	True	77.665	162	563	95	below_threshold
Campylobacter lanienae	strain=NCTC 13004	GCA_002139935.1	75658	75658	type	True	77.4005	64	563	95	below_threshold
Campylobacter blaseri	strain=LMG 30333	GCA_013201895.1	2042961	2042961	type	True	77.3997	172	563	95	below_threshold
Campylobacter geochelonis	strain=RC20	GCA_900063025.1	1780362	1780362	type	True	77.3434	157	563	95	below_threshold
Campylobacter jejuni	strain=NCTC11351	GCA_001457695.1	197	197	type	True	77.3396	58	563	95	below_threshold
Campylobacter blaseri	strain=17S00004-5	GCA_003015205.1	2042961	2042961	type	True	77.2186	169	563	95	below_threshold
Campylobacter hepaticus	strain=HV10	GCA_001687475.2	1813019	1813019	type	True	77.1993	53	563	95	below_threshold
Campylobacter coli	strain=LMG 9860	GCA_000254135.2	195	195	type	True	76.475	53	563	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=CCUG 11284	GCA_008802045.1	32022	197	type	True	76.4278	55	563	95	below_threshold
Campylobacter jejuni subsp. jejuni	strain=ATCC 33560	GCA_000254515.2	32022	197	type	True	76.3135	52	563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:43,315] [INFO] DFAST Taxonomy check result was written to GCF_013201645.1_ASM1320164v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:43,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:43,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:43,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference/checkm_data
[2024-01-24 13:18:43,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:43,339] [INFO] Task started: CheckM
[2024-01-24 13:18:43,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201645.1_ASM1320164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201645.1_ASM1320164v1_genomic.fna/checkm_input GCF_013201645.1_ASM1320164v1_genomic.fna/checkm_result
[2024-01-24 13:19:00,939] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:00,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,971] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:00,971] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:00,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201645.1_ASM1320164v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:00,972] [INFO] Task started: Blastn
[2024-01-24 13:19:00,972] [INFO] Running command: blastn -query GCF_013201645.1_ASM1320164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c594e5-84c4-46c1-b457-77ae020dbce9/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201645.1_ASM1320164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:01,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:01,886] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:01,886] [INFO] Target genome list was writen to GCF_013201645.1_ASM1320164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:01,910] [INFO] Task started: fastANI
[2024-01-24 13:19:01,910] [INFO] Running command: fastANI --query /var/lib/cwl/stge7c6473a-1a91-4027-b4bb-779a025659ac/GCF_013201645.1_ASM1320164v1_genomic.fna.gz --refList GCF_013201645.1_ASM1320164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201645.1_ASM1320164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:09,031] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:09,044] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:09,044] [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_013201645.1	s__Campylobacter_B corcagiensis	100.0	561	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_000413435.1	s__Campylobacter_B ureolyticus_A	78.3645	245	563	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_013372225.1	s__Campylobacter_B ureolyticus	78.0606	233	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	97.14	95.63	0.91	0.85	10	-
GCF_000816245.1	s__Campylobacter_D sp000816245	77.9524	68	563	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_012728225.1	s__Campylobacter_B sp012728225	77.8931	196	563	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	77.7679	175	563	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_008245005.1	s__Campylobacter_B sputorum	77.6702	123	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.49	98.05	0.98	0.93	7	-
GCF_013201685.1	s__Campylobacter_B geochelonis	77.5963	160	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B	95.0	99.40	99.12	0.97	0.95	4	-
GCA_012519705.1	s__Campylobacter_B sp012519705	77.4674	191	563	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_013201895.1	s__Campylobacter_B blaseri	77.2833	173	563	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_002139915.1	s__Campylobacter sp002139915	77.1407	74	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter	95.0	97.90	97.72	0.92	0.90	37	-
GCF_002022005.1	s__Campylobacter_A caledonicus	77.0281	80	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A	95.0	99.31	99.26	0.98	0.97	3	-
GCF_002179635.1	s__Campylobacter_D jejuni_C	76.3936	77	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.56	98.44	0.93	0.93	4	-
GCF_016599045.1	s__Campylobacter_D sp016599045	76.1733	66	563	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.00	98.98	0.95	0.93	3	-
GCA_017646085.1	s__Campylobacter sp017646085	76.1598	62	563	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 13:19:09,046] [INFO] GTDB search result was written to GCF_013201645.1_ASM1320164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:09,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:09,051] [INFO] DFAST_QC result json was written to GCF_013201645.1_ASM1320164v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:09,051] [INFO] DFAST_QC completed!
[2024-01-24 13:19:09,051] [INFO] Total running time: 0h0m36s