[2024-01-24 13:57:57,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference
[2024-01-24 13:57:58,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,917] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c396d2e-5709-4ca4-bb30-6b48d58107fb/GCF_001704115.1_ASM170411v1_genomic.fna.gz | prodigal -d GCF_001704115.1_ASM170411v1_genomic.fna/cds.fna -a GCF_001704115.1_ASM170411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:09,216] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:09,216] [INFO] Task started: HMMsearch
[2024-01-24 13:58:09,216] [INFO] Running command: hmmsearch --tblout GCF_001704115.1_ASM170411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference/reference_markers.hmm GCF_001704115.1_ASM170411v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:09,562] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:09,564] [INFO] Found 6/6 markers.
[2024-01-24 13:58:09,617] [INFO] Query marker FASTA was written to GCF_001704115.1_ASM170411v1_genomic.fna/markers.fasta
[2024-01-24 13:58:09,617] [INFO] Task started: Blastn
[2024-01-24 13:58:09,617] [INFO] Running command: blastn -query GCF_001704115.1_ASM170411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference/reference_markers.fasta -out GCF_001704115.1_ASM170411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:10,355] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:10,358] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:10,358] [INFO] Target genome list was writen to GCF_001704115.1_ASM170411v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:10,484] [INFO] Task started: fastANI
[2024-01-24 13:58:10,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c396d2e-5709-4ca4-bb30-6b48d58107fb/GCF_001704115.1_ASM170411v1_genomic.fna.gz --refList GCF_001704115.1_ASM170411v1_genomic.fna/target_genomes.txt --output GCF_001704115.1_ASM170411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:27,426] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:27,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:27,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:27,448] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:27,449] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:27,449] [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
Acinetobacter larvae	strain=BRTC-1	GCA_001704115.1	1789224	1789224	type	True	100.0	1246	1247	95	conclusive
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.0718	246	1247	95	below_threshold
Acinetobacter pullicarnis	strain=S23	GCA_006352475.1	2576829	2576829	type	True	78.9141	363	1247	95	below_threshold
Acinetobacter bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	78.7851	299	1247	95	below_threshold
Acinetobacter rudis	strain=DSM 24031	GCA_000829675.1	632955	632955	type	True	78.7636	309	1247	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	78.7439	309	1247	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.7022	246	1247	95	below_threshold
Acinetobacter towneri	strain=CIP 107472	GCA_000368785.1	202956	202956	type	True	78.5925	285	1247	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.5848	237	1247	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	78.4999	255	1247	95	below_threshold
Acinetobacter brisouii	strain=DSM 18516	GCA_000931655.1	396323	396323	type	True	78.4472	210	1247	95	below_threshold
Acinetobacter towneri	strain=DSM 14962	GCA_000688495.1	202956	202956	type	True	78.4148	272	1247	95	below_threshold
Acinetobacter seohaensis	strain=DSM 16313	GCA_018403785.1	281376	281376	type	True	78.3976	268	1247	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.3554	291	1247	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.3453	297	1247	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	78.3389	286	1247	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	78.3114	270	1247	95	below_threshold
Acinetobacter tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	78.2942	257	1247	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	78.2794	302	1247	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	78.2486	294	1247	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	78.1609	296	1247	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	78.0827	265	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:27,451] [INFO] DFAST Taxonomy check result was written to GCF_001704115.1_ASM170411v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:27,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:27,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:27,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference/checkm_data
[2024-01-24 13:58:27,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:27,493] [INFO] Task started: CheckM
[2024-01-24 13:58:27,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001704115.1_ASM170411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001704115.1_ASM170411v1_genomic.fna/checkm_input GCF_001704115.1_ASM170411v1_genomic.fna/checkm_result
[2024-01-24 13:59:04,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:04,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,845] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:04,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:04,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001704115.1_ASM170411v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:04,847] [INFO] Task started: Blastn
[2024-01-24 13:59:04,847] [INFO] Running command: blastn -query GCF_001704115.1_ASM170411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88425375-22ef-4b68-8f33-a4915c2f53aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_001704115.1_ASM170411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:05,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:05,973] [INFO] Selected 23 target genomes.
[2024-01-24 13:59:05,973] [INFO] Target genome list was writen to GCF_001704115.1_ASM170411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:06,035] [INFO] Task started: fastANI
[2024-01-24 13:59:06,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c396d2e-5709-4ca4-bb30-6b48d58107fb/GCF_001704115.1_ASM170411v1_genomic.fna.gz --refList GCF_001704115.1_ASM170411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001704115.1_ASM170411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:21,470] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:21,492] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:21,492] [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_001704115.1	s__Acinetobacter larvae	100.0	1246	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001307195.1	s__Acinetobacter equi	79.2008	229	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015218165.1	s__Acinetobacter piscicola_A	79.1036	305	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_006352475.1	s__Acinetobacter pullicarnis	78.986	364	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013343215.1	s__Acinetobacter lwoffii_C	78.9426	215	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.90	0.93	0.91	5	-
GCF_004345325.1	s__Acinetobacter calcoaceticus_D	78.8712	317	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368925.1	s__Acinetobacter bereziniae	78.8491	299	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCF_001758345.1	s__Acinetobacter towneri_A	78.8322	248	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.24	97.24	0.85	0.85	2	-
GCF_000368565.1	s__Acinetobacter gerneri	78.8029	311	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	-
GCF_000829675.1	s__Acinetobacter rudis	78.7777	308	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900323515.1	s__Acinetobacter stercoris	78.7025	245	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_000368785.1	s__Acinetobacter towneri	78.5989	286	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.88	97.09	0.88	0.84	48	-
GCF_004331035.1	s__Acinetobacter sp004331035	78.5506	265	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331175.1	s__Acinetobacter sp004331175	78.5388	255	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939195.1	s__Acinetobacter kanungonis	78.5081	281	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_000400735.1	s__Acinetobacter tandoii	78.3622	271	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_002233755.1	s__Acinetobacter piscicola	78.3491	286	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336635.1	s__Acinetobacter sp004336635	78.3475	266	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_003024515.2	s__Acinetobacter sichuanensis	78.2686	303	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135235.1	s__Acinetobacter sp002135235	78.2323	295	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	78.1806	276	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296655.1	s__Acinetobacter sp002296655	78.0983	234	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
GCF_001707755.1	s__Acinetobacter celticus	78.0951	264	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:21,494] [INFO] GTDB search result was written to GCF_001704115.1_ASM170411v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:21,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:21,499] [INFO] DFAST_QC result json was written to GCF_001704115.1_ASM170411v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:21,499] [INFO] DFAST_QC completed!
[2024-01-24 13:59:21,499] [INFO] Total running time: 0h1m24s