[2024-01-24 12:30:51,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:51,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:51,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference
[2024-01-24 12:30:52,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:52,709] [INFO] Task started: Prodigal
[2024-01-24 12:30:52,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ec8ae96-f92b-42ff-a073-ce98a33e5644/GCF_000248295.1_ASM24829v2_genomic.fna.gz | prodigal -d GCF_000248295.1_ASM24829v2_genomic.fna/cds.fna -a GCF_000248295.1_ASM24829v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:02,938] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:02,939] [INFO] Task started: HMMsearch
[2024-01-24 12:31:02,939] [INFO] Running command: hmmsearch --tblout GCF_000248295.1_ASM24829v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference/reference_markers.hmm GCF_000248295.1_ASM24829v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:03,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:03,264] [INFO] Found 6/6 markers.
[2024-01-24 12:31:03,309] [INFO] Query marker FASTA was written to GCF_000248295.1_ASM24829v2_genomic.fna/markers.fasta
[2024-01-24 12:31:03,310] [INFO] Task started: Blastn
[2024-01-24 12:31:03,310] [INFO] Running command: blastn -query GCF_000248295.1_ASM24829v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference/reference_markers.fasta -out GCF_000248295.1_ASM24829v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,933] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,937] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:03,938] [INFO] Target genome list was writen to GCF_000248295.1_ASM24829v2_genomic.fna/target_genomes.txt
[2024-01-24 12:31:03,941] [INFO] Task started: fastANI
[2024-01-24 12:31:03,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ec8ae96-f92b-42ff-a073-ce98a33e5644/GCF_000248295.1_ASM24829v2_genomic.fna.gz --refList GCF_000248295.1_ASM24829v2_genomic.fna/target_genomes.txt --output GCF_000248295.1_ASM24829v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:14,435] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:14,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:14,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:14,453] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:14,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:14,453] [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 bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	99.9628	1485	1494	95	conclusive
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	83.8307	1026	1494	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	83.7515	1036	1494	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	82.9092	737	1494	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	82.3678	664	1494	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	81.9686	768	1494	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	81.7422	674	1494	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.9607	496	1494	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	79.601	445	1494	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.4618	361	1494	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.2632	358	1494	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.1798	411	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:14,455] [INFO] DFAST Taxonomy check result was written to GCF_000248295.1_ASM24829v2_genomic.fna/tc_result.tsv
[2024-01-24 12:31:14,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:14,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:14,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference/checkm_data
[2024-01-24 12:31:14,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:14,503] [INFO] Task started: CheckM
[2024-01-24 12:31:14,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000248295.1_ASM24829v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000248295.1_ASM24829v2_genomic.fna/checkm_input GCF_000248295.1_ASM24829v2_genomic.fna/checkm_result
[2024-01-24 12:31:51,040] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:51,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,059] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:51,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:51,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000248295.1_ASM24829v2_genomic.fna/markers.fasta)
[2024-01-24 12:31:51,060] [INFO] Task started: Blastn
[2024-01-24 12:31:51,060] [INFO] Running command: blastn -query GCF_000248295.1_ASM24829v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d2a9d37-9f1a-42f7-8471-cf33b70bfa59/dqc_reference/reference_markers_gtdb.fasta -out GCF_000248295.1_ASM24829v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:51,950] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:51,953] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:51,953] [INFO] Target genome list was writen to GCF_000248295.1_ASM24829v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:51,964] [INFO] Task started: fastANI
[2024-01-24 12:31:51,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ec8ae96-f92b-42ff-a073-ce98a33e5644/GCF_000248295.1_ASM24829v2_genomic.fna.gz --refList GCF_000248295.1_ASM24829v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000248295.1_ASM24829v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:03,600] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:03,614] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:03,614] [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_000368925.1	s__Acinetobacter bereziniae	99.9628	1486	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	conclusive
GCA_009912575.1	s__Acinetobacter bereziniae_A	90.7915	1058	1494	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	90.0207	1075	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.90	99.88	0.97	0.96	14	-
GCF_000368145.1	s__Acinetobacter guillouiae	83.7346	1039	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_003611475.1	s__Acinetobacter rongchengensis	82.9014	738	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024515.2	s__Acinetobacter sichuanensis	82.3565	665	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696605.3	s__Acinetobacter wuhouensis	82.0245	759	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_002233755.1	s__Acinetobacter piscicola	81.7382	674	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214135.1	s__Acinetobacter sp000214135	81.6522	708	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268395.1	s__Acinetobacter sp003268395	80.6959	583	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809855.1	s__Acinetobacter sp902809855	80.6133	545	1494	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 12:32:03,616] [INFO] GTDB search result was written to GCF_000248295.1_ASM24829v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:03,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:03,619] [INFO] DFAST_QC result json was written to GCF_000248295.1_ASM24829v2_genomic.fna/dqc_result.json
[2024-01-24 12:32:03,619] [INFO] DFAST_QC completed!
[2024-01-24 12:32:03,619] [INFO] Total running time: 0h1m12s