[2024-01-24 12:29:28,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference
[2024-01-24 12:29:29,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,910] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,910] [INFO] Running command: gunzip -c /var/lib/cwl/stgf54ba5b5-c018-41c4-8a91-35592f843fcd/GCF_006352475.1_ASM635247v1_genomic.fna.gz | prodigal -d GCF_006352475.1_ASM635247v1_genomic.fna/cds.fna -a GCF_006352475.1_ASM635247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:40,192] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:40,192] [INFO] Task started: HMMsearch
[2024-01-24 12:29:40,192] [INFO] Running command: hmmsearch --tblout GCF_006352475.1_ASM635247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference/reference_markers.hmm GCF_006352475.1_ASM635247v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:40,567] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:40,569] [INFO] Found 6/6 markers.
[2024-01-24 12:29:40,604] [INFO] Query marker FASTA was written to GCF_006352475.1_ASM635247v1_genomic.fna/markers.fasta
[2024-01-24 12:29:40,604] [INFO] Task started: Blastn
[2024-01-24 12:29:40,604] [INFO] Running command: blastn -query GCF_006352475.1_ASM635247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference/reference_markers.fasta -out GCF_006352475.1_ASM635247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:41,434] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:41,437] [INFO] Selected 22 target genomes.
[2024-01-24 12:29:41,437] [INFO] Target genome list was writen to GCF_006352475.1_ASM635247v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:41,448] [INFO] Task started: fastANI
[2024-01-24 12:29:41,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgf54ba5b5-c018-41c4-8a91-35592f843fcd/GCF_006352475.1_ASM635247v1_genomic.fna.gz --refList GCF_006352475.1_ASM635247v1_genomic.fna/target_genomes.txt --output GCF_006352475.1_ASM635247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:57,697] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:57,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:57,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:57,715] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:57,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:57,715] [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 pullicarnis	strain=S23	GCA_006352475.1	2576829	2576829	type	True	100.0	1367	1373	95	conclusive
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	80.1302	395	1373	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.0038	380	1373	95	below_threshold
Acinetobacter rudis	strain=CIP 110305	GCA_000413895.1	632955	632955	type	True	79.3859	405	1373	95	below_threshold
Acinetobacter tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	79.361	359	1373	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	79.3379	387	1373	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	79.3291	415	1373	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	79.2893	423	1373	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	79.2283	437	1373	95	below_threshold
Acinetobacter rudis	strain=DSM 24031	GCA_000829675.1	632955	632955	type	True	78.9869	392	1373	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.9702	410	1373	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	78.9362	401	1373	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.9002	399	1373	95	below_threshold
Acinetobacter larvae	strain=BRTC-1	GCA_001704115.1	1789224	1789224	type	True	78.8955	361	1373	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	78.7656	305	1373	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.7262	305	1373	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	78.674	328	1373	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	78.6694	332	1373	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	78.5065	336	1373	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	78.5048	287	1373	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	78.4406	262	1373	95	below_threshold
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	78.17	285	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:57,717] [INFO] DFAST Taxonomy check result was written to GCF_006352475.1_ASM635247v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:57,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:57,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:57,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference/checkm_data
[2024-01-24 12:29:57,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:57,759] [INFO] Task started: CheckM
[2024-01-24 12:29:57,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006352475.1_ASM635247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006352475.1_ASM635247v1_genomic.fna/checkm_input GCF_006352475.1_ASM635247v1_genomic.fna/checkm_result
[2024-01-24 12:30:35,012] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:35,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:35,036] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:35,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:35,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006352475.1_ASM635247v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:35,037] [INFO] Task started: Blastn
[2024-01-24 12:30:35,037] [INFO] Running command: blastn -query GCF_006352475.1_ASM635247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c0bf19e-4a69-4b06-9576-3c8d746f8704/dqc_reference/reference_markers_gtdb.fasta -out GCF_006352475.1_ASM635247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:36,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:36,199] [INFO] Selected 22 target genomes.
[2024-01-24 12:30:36,199] [INFO] Target genome list was writen to GCF_006352475.1_ASM635247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:36,232] [INFO] Task started: fastANI
[2024-01-24 12:30:36,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgf54ba5b5-c018-41c4-8a91-35592f843fcd/GCF_006352475.1_ASM635247v1_genomic.fna.gz --refList GCF_006352475.1_ASM635247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006352475.1_ASM635247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:52,371] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:52,389] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:52,389] [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_006352475.1	s__Acinetobacter pullicarnis	100.0	1369	1373	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_000368045.1	s__Acinetobacter johnsonii	79.8955	378	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_015218165.1	s__Acinetobacter piscicola_A	79.6638	442	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_004345325.1	s__Acinetobacter calcoaceticus_D	79.6624	561	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012371325.1	s__Acinetobacter sp012371325	79.577	327	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCF_000368565.1	s__Acinetobacter gerneri	79.3283	415	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	-
GCF_001696605.3	s__Acinetobacter wuhouensis	79.2	439	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_900107285.1	s__Acinetobacter kyonggiensis	79.1861	415	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCF_013004375.1	s__Acinetobacter terrae	79.1189	352	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_000829675.1	s__Acinetobacter rudis	78.9869	392	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	78.9833	329	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704115.1	s__Acinetobacter larvae	78.957	361	1373	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	78.9362	401	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632455.1	s__Acinetobacter sp000632455	78.8947	292	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.93	97.36	0.88	0.86	4	-
GCF_002135345.1	s__Acinetobacter sp002135345	78.8805	381	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135335.1	s__Acinetobacter sp002135335	78.8561	381	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016508585.1	s__Acinetobacter baumannii_B	78.7669	349	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.90	99.88	0.97	0.96	14	-
GCF_004331035.1	s__Acinetobacter sp004331035	78.7597	339	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135205.1	s__Acinetobacter sp002135205	78.7291	338	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
GCF_001678755.1	s__Acinetobacter gandensis	78.6784	331	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCA_900766635.1	s__Acinetobacter sp900766635	78.5024	185	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368685.1	s__Acinetobacter baylyi	78.4291	288	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:52,391] [INFO] GTDB search result was written to GCF_006352475.1_ASM635247v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:52,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:52,397] [INFO] DFAST_QC result json was written to GCF_006352475.1_ASM635247v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:52,397] [INFO] DFAST_QC completed!
[2024-01-24 12:30:52,398] [INFO] Total running time: 0h1m24s