[2024-01-24 12:51:05,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference
[2024-01-24 12:51:06,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,700] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg3097eef3-de6f-439d-8082-15b3e5e77275/GCF_006757745.1_ASM675774v1_genomic.fna.gz | prodigal -d GCF_006757745.1_ASM675774v1_genomic.fna/cds.fna -a GCF_006757745.1_ASM675774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:14,007] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:14,007] [INFO] Task started: HMMsearch
[2024-01-24 12:51:14,007] [INFO] Running command: hmmsearch --tblout GCF_006757745.1_ASM675774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference/reference_markers.hmm GCF_006757745.1_ASM675774v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:14,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:14,289] [INFO] Found 6/6 markers.
[2024-01-24 12:51:14,321] [INFO] Query marker FASTA was written to GCF_006757745.1_ASM675774v1_genomic.fna/markers.fasta
[2024-01-24 12:51:14,321] [INFO] Task started: Blastn
[2024-01-24 12:51:14,321] [INFO] Running command: blastn -query GCF_006757745.1_ASM675774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference/reference_markers.fasta -out GCF_006757745.1_ASM675774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:14,966] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:14,970] [INFO] Selected 33 target genomes.
[2024-01-24 12:51:14,970] [INFO] Target genome list was writen to GCF_006757745.1_ASM675774v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:14,995] [INFO] Task started: fastANI
[2024-01-24 12:51:14,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg3097eef3-de6f-439d-8082-15b3e5e77275/GCF_006757745.1_ASM675774v1_genomic.fna.gz --refList GCF_006757745.1_ASM675774v1_genomic.fna/target_genomes.txt --output GCF_006757745.1_ASM675774v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:35,769] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:35,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:35,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:35,801] [INFO] Found 28 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:51:35,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:35,802] [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 radioresistens	strain=NBRC 102413	GCA_006757745.1	40216	40216	type	True	100.0	1137	1139	95	conclusive
Acinetobacter radioresistens	strain=CIP 103788	GCA_000368905.1	40216	40216	type	True	99.9751	1045	1139	95	conclusive
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	80.9514	395	1139	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	80.5741	407	1139	95	below_threshold
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	80.3683	387	1139	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	80.368	322	1139	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	80.2302	391	1139	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.707	380	1139	95	below_threshold
Acinetobacter seohaensis	strain=DSM 16313	GCA_018403785.1	281376	281376	type	True	79.6641	308	1139	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.662	337	1139	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.6562	334	1139	95	below_threshold
Acinetobacter towneri	strain=CIP 107472	GCA_000368785.1	202956	202956	type	True	79.6463	326	1139	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	79.4765	355	1139	95	below_threshold
Acinetobacter towneri	strain=DSM 14962	GCA_000688495.1	202956	202956	type	True	79.4443	309	1139	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	79.3517	362	1139	95	below_threshold
Acinetobacter pullicarnis	strain=S23	GCA_006352475.1	2576829	2576829	type	True	79.3337	263	1139	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	79.0997	282	1139	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	79.0033	306	1139	95	below_threshold
Acinetobacter brisouii	strain=CIP 110357	GCA_000488275.1	396323	396323	type	True	78.9979	263	1139	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	78.9516	340	1139	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	78.9307	276	1139	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	78.8756	284	1139	95	below_threshold
Acinetobacter bouvetii	strain=CIP 107468	GCA_000368865.1	202951	202951	type	True	78.8599	299	1139	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	78.7035	277	1139	95	below_threshold
Acinetobacter bouvetii	strain=DSM 14964	GCA_000373725.1	202951	202951	type	True	78.6593	306	1139	95	below_threshold
Acinetobacter brisouii	strain=DSM 18516	GCA_000931655.1	396323	396323	type	True	78.6197	253	1139	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	78.6135	257	1139	95	below_threshold
Acinetobacter halotolerans	strain=JCM 31009	GCA_004208515.1	1752076	1752076	type	True	78.6114	245	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:35,803] [INFO] DFAST Taxonomy check result was written to GCF_006757745.1_ASM675774v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:35,804] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:35,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:35,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference/checkm_data
[2024-01-24 12:51:35,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:35,840] [INFO] Task started: CheckM
[2024-01-24 12:51:35,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006757745.1_ASM675774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006757745.1_ASM675774v1_genomic.fna/checkm_input GCF_006757745.1_ASM675774v1_genomic.fna/checkm_result
[2024-01-24 12:52:03,720] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:03,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:03,740] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:03,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:03,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006757745.1_ASM675774v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:03,741] [INFO] Task started: Blastn
[2024-01-24 12:52:03,742] [INFO] Running command: blastn -query GCF_006757745.1_ASM675774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea51292a-62ed-4460-92b9-0a766a376b34/dqc_reference/reference_markers_gtdb.fasta -out GCF_006757745.1_ASM675774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:04,575] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:04,580] [INFO] Selected 34 target genomes.
[2024-01-24 12:52:04,580] [INFO] Target genome list was writen to GCF_006757745.1_ASM675774v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:04,631] [INFO] Task started: fastANI
[2024-01-24 12:52:04,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg3097eef3-de6f-439d-8082-15b3e5e77275/GCF_006757745.1_ASM675774v1_genomic.fna.gz --refList GCF_006757745.1_ASM675774v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006757745.1_ASM675774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:25,918] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:25,956] [INFO] Found 33 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:25,956] [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_006757745.1	s__Acinetobacter radioresistens	100.0	1137	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.57	97.95	0.93	0.87	74	conclusive
GCF_000488255.1	s__Acinetobacter indicus	80.8833	393	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	-
GCF_015218165.1	s__Acinetobacter piscicola_A	80.8168	328	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.43	98.21	0.96	0.90	7	-
GCF_000369625.1	s__Acinetobacter variabilis	80.5988	407	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.87	95.07	0.88	0.83	48	-
GCF_000214135.1	s__Acinetobacter sp000214135	80.2722	293	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165255.2	s__Acinetobacter sp002165255	80.1043	278	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000773685.1	s__Acinetobacter sp000773685	79.9145	308	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368785.1	s__Acinetobacter towneri	79.6424	325	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.88	97.09	0.88	0.84	48	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	79.6136	363	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368145.1	s__Acinetobacter guillouiae	79.4874	318	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	79.4793	355	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_000400735.1	s__Acinetobacter tandoii	79.3874	362	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_002165375.2	s__Acinetobacter chinensis	79.3816	372	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.92	0.89	0.89	2	-
GCF_000196795.1	s__Acinetobacter oleivorans	79.3768	317	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_000399685.1	s__Acinetobacter pittii_E	79.3562	326	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368265.1	s__Acinetobacter sp000368265	79.1786	262	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.84	96.49	0.89	0.85	3	-
GCF_006352475.1	s__Acinetobacter pullicarnis	79.1635	260	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647545.1	s__Acinetobacter sp001647545	79.1505	353	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.85	96.85	0.89	0.89	2	-
GCF_002018365.1	s__Acinetobacter sp002018365	79.1134	294	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_000369805.1	s__Acinetobacter sp000369805	79.1074	277	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002233755.1	s__Acinetobacter piscicola	79.0832	283	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369405.1	s__Acinetobacter sp000369405	79.0228	288	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000488275.1	s__Acinetobacter brisouii	78.999	264	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.72	96.16	0.96	0.91	4	-
GCF_013344765.1	s__Acinetobacter lactucae_A	78.9489	297	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_009939195.1	s__Acinetobacter kanungonis	78.8953	335	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_000368865.1	s__Acinetobacter bouvetii	78.8922	298	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.30	95.72	0.97	0.92	6	-
GCF_003611475.1	s__Acinetobacter rongchengensis	78.8762	285	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001605885.1	s__Acinetobacter lactucae	78.8109	327	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_009372255.1	s__Acinetobacter guerrae	78.7812	309	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	98.41	0.90	0.89	3	-
GCF_000368585.1	s__Acinetobacter venetianus	78.7347	274	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_004331255.1	s__Acinetobacter sp004331255	78.7337	332	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105055.1	s__Acinetobacter sp003105055	78.6524	328	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208515.1	s__Acinetobacter halotolerans	78.6179	244	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:25,958] [INFO] GTDB search result was written to GCF_006757745.1_ASM675774v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:25,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:25,965] [INFO] DFAST_QC result json was written to GCF_006757745.1_ASM675774v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:25,965] [INFO] DFAST_QC completed!
[2024-01-24 12:52:25,966] [INFO] Total running time: 0h1m20s