[2024-01-24 12:53:49,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference
[2024-01-24 12:53:51,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,734] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,734] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f7abce9-677d-4788-beeb-b5ccb7f54a03/GCF_000092245.1_ASM9224v1_genomic.fna.gz | prodigal -d GCF_000092245.1_ASM9224v1_genomic.fna/cds.fna -a GCF_000092245.1_ASM9224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:57,010] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:57,011] [INFO] Task started: HMMsearch
[2024-01-24 12:53:57,011] [INFO] Running command: hmmsearch --tblout GCF_000092245.1_ASM9224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference/reference_markers.hmm GCF_000092245.1_ASM9224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:57,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:57,265] [INFO] Found 6/6 markers.
[2024-01-24 12:53:57,292] [INFO] Query marker FASTA was written to GCF_000092245.1_ASM9224v1_genomic.fna/markers.fasta
[2024-01-24 12:53:57,293] [INFO] Task started: Blastn
[2024-01-24 12:53:57,293] [INFO] Running command: blastn -query GCF_000092245.1_ASM9224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference/reference_markers.fasta -out GCF_000092245.1_ASM9224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:58,518] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:58,523] [INFO] Selected 22 target genomes.
[2024-01-24 12:53:58,523] [INFO] Target genome list was writen to GCF_000092245.1_ASM9224v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:58,745] [INFO] Task started: fastANI
[2024-01-24 12:53:58,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7abce9-677d-4788-beeb-b5ccb7f54a03/GCF_000092245.1_ASM9224v1_genomic.fna.gz --refList GCF_000092245.1_ASM9224v1_genomic.fna/target_genomes.txt --output GCF_000092245.1_ASM9224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:10,486] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:10,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:10,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:10,505] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:10,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:10,505] [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
Arcobacter nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	100.0	1063	1064	95	conclusive
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	79.7905	470	1064	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	79.6695	445	1064	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	79.5726	398	1064	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	79.472	389	1064	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.4582	416	1064	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	79.359	354	1064	95	below_threshold
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	79.3377	349	1064	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	79.3307	383	1064	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	79.2977	400	1064	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	79.197	418	1064	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	79.1605	382	1064	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	79.1041	401	1064	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	79.069	396	1064	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	79.0228	396	1064	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	79.0145	429	1064	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	78.9451	422	1064	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	78.888	420	1064	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	78.781	417	1064	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	78.7702	412	1064	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	78.2281	266	1064	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	77.9204	283	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:10,507] [INFO] DFAST Taxonomy check result was written to GCF_000092245.1_ASM9224v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:10,508] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:10,508] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:10,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference/checkm_data
[2024-01-24 12:54:10,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:10,547] [INFO] Task started: CheckM
[2024-01-24 12:54:10,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092245.1_ASM9224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092245.1_ASM9224v1_genomic.fna/checkm_input GCF_000092245.1_ASM9224v1_genomic.fna/checkm_result
[2024-01-24 12:54:33,811] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:33,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:33,836] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:33,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:33,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092245.1_ASM9224v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:33,837] [INFO] Task started: Blastn
[2024-01-24 12:54:33,838] [INFO] Running command: blastn -query GCF_000092245.1_ASM9224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b42520b-3d46-492d-9683-f298bfe70935/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092245.1_ASM9224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:34,646] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:34,650] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:34,650] [INFO] Target genome list was writen to GCF_000092245.1_ASM9224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:34,666] [INFO] Task started: fastANI
[2024-01-24 12:54:34,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7abce9-677d-4788-beeb-b5ccb7f54a03/GCF_000092245.1_ASM9224v1_genomic.fna.gz --refList GCF_000092245.1_ASM9224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092245.1_ASM9224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:44,374] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:44,388] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:44,389] [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_000092245.1	s__Arcobacter nitrofigilis	100.0	1063	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004116465.1	s__Arcobacter sp004116465	91.9681	860	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869535.1	s__Arcobacter sp002869535	84.8886	667	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	79.977	484	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201665.1	s__Aliarcobacter venerupis	79.8087	470	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003544815.1	s__Aliarcobacter suis	79.5297	400	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544935.1	s__Malaciobacter molluscorum	79.5084	416	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCF_900187115.1	s__Aliarcobacter butzleri	79.332	347	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_003346815.1	s__Halarcobacter bivalviorum	79.3239	382	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCA_004116495.1	s__Malaciobacter sp004116495	79.2324	429	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252105.1	s__Halarcobacter sp003252105	79.1897	403	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346775.1	s__Malaciobacter mytili	78.9697	422	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCF_009208075.1	s__Poseidonibacter sp009208075	78.8783	375	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_013201825.1	s__Halarcobacter ebronensis	78.7983	421	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCA_001655195.1	s__Arcobacter_A sp001655195	78.3875	278	1064	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:44,391] [INFO] GTDB search result was written to GCF_000092245.1_ASM9224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:44,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:44,396] [INFO] DFAST_QC result json was written to GCF_000092245.1_ASM9224v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:44,396] [INFO] DFAST_QC completed!
[2024-01-24 12:54:44,396] [INFO] Total running time: 0h0m55s