[2023-03-18 00:15:08,417] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:15:08,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:15:08,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference
[2023-03-18 00:15:09,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:15:09,502] [INFO] Task started: Prodigal
[2023-03-18 00:15:09,502] [INFO] Running command: cat /var/lib/cwl/stge55db784-b481-4814-95dd-87648e2b8ba7/OceanDNA-b38575.fa | prodigal -d OceanDNA-b38575/cds.fna -a OceanDNA-b38575/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:15:28,024] [INFO] Task succeeded: Prodigal
[2023-03-18 00:15:28,025] [INFO] Task started: HMMsearch
[2023-03-18 00:15:28,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b38575/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference/reference_markers.hmm OceanDNA-b38575/protein.faa > /dev/null
[2023-03-18 00:15:28,235] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:15:28,236] [INFO] Found 6/6 markers.
[2023-03-18 00:15:28,263] [INFO] Query marker FASTA was written to OceanDNA-b38575/markers.fasta
[2023-03-18 00:15:28,264] [INFO] Task started: Blastn
[2023-03-18 00:15:28,264] [INFO] Running command: blastn -query OceanDNA-b38575/markers.fasta -db /var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference/reference_markers.fasta -out OceanDNA-b38575/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:28,847] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:28,848] [INFO] Selected 9 target genomes.
[2023-03-18 00:15:28,848] [INFO] Target genome list was writen to OceanDNA-b38575/target_genomes.txt
[2023-03-18 00:15:28,855] [INFO] Task started: fastANI
[2023-03-18 00:15:28,855] [INFO] Running command: fastANI --query /var/lib/cwl/stge55db784-b481-4814-95dd-87648e2b8ba7/OceanDNA-b38575.fa --refList OceanDNA-b38575/target_genomes.txt --output OceanDNA-b38575/fastani_result.tsv --threads 1
[2023-03-18 00:15:35,949] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:35,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:15:35,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:15:35,956] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2023-03-18 00:15:35,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 00:15:35,956] [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 pittii	strain=CIP 70.29	GCA_000369045.1	48296	48296	type	True	96.9527	1044	1165	95	conclusive
Acinetobacter pittii	strain=DSM 25618	GCA_000836015.1	48296	48296	type	True	96.8791	1062	1165	95	conclusive
Acinetobacter pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	96.8643	1071	1165	95	conclusive
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	96.6448	1040	1165	95	conclusive
Acinetobacter lactucae	strain=NRRL B-41902	GCA_001605885.1	1785128	1785128	type	True	93.3074	997	1165	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	88.8219	972	1165	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	88.7966	977	1165	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.5601	444	1165	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:15:35,957] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38575/tc_result.tsv
[2023-03-18 00:15:35,957] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:15:35,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:15:35,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference/checkm_data
[2023-03-18 00:15:35,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:15:35,972] [INFO] Task started: CheckM
[2023-03-18 00:15:35,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38575/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38575/checkm_input OceanDNA-b38575/checkm_result
[2023-03-18 00:16:24,011] [INFO] Task succeeded: CheckM
[2023-03-18 00:16:24,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.90%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 00:16:24,122] [INFO] ===== Completeness check finished =====
[2023-03-18 00:16:24,123] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:16:24,123] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38575/markers.fasta)
[2023-03-18 00:16:24,124] [INFO] Task started: Blastn
[2023-03-18 00:16:24,124] [INFO] Running command: blastn -query OceanDNA-b38575/markers.fasta -db /var/lib/cwl/stg471a14af-e393-4fed-ab6c-ca5af03212f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38575/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:16:24,918] [INFO] Task succeeded: Blastn
[2023-03-18 00:16:24,920] [INFO] Selected 11 target genomes.
[2023-03-18 00:16:24,920] [INFO] Target genome list was writen to OceanDNA-b38575/target_genomes_gtdb.txt
[2023-03-18 00:16:24,935] [INFO] Task started: fastANI
[2023-03-18 00:16:24,935] [INFO] Running command: fastANI --query /var/lib/cwl/stge55db784-b481-4814-95dd-87648e2b8ba7/OceanDNA-b38575.fa --refList OceanDNA-b38575/target_genomes_gtdb.txt --output OceanDNA-b38575/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:16:32,904] [INFO] Task succeeded: fastANI
[2023-03-18 00:16:32,911] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:16:32,911] [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_000369045.1	s__Acinetobacter pittii	96.9527	1044	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	conclusive
GCF_013009345.1	s__Acinetobacter sp013009345	94.4938	989	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	-
GCF_002928115.1	s__Acinetobacter pittii_H	94.3884	986	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_001605885.1	s__Acinetobacter lactucae	93.3074	997	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_013344765.1	s__Acinetobacter lactucae_A	92.7378	829	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_000399685.1	s__Acinetobacter pittii_E	92.2262	968	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368765.1	s__Acinetobacter junii	79.5612	446	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_011058205.1	s__Acinetobacter fasciculus	79.1811	280	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCA_002296655.1	s__Acinetobacter sp002296655	78.4269	280	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
GCF_009557235.1	s__Acinetobacter wanghuae	78.4109	269	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:16:32,911] [INFO] GTDB search result was written to OceanDNA-b38575/result_gtdb.tsv
[2023-03-18 00:16:32,911] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:16:32,912] [INFO] DFAST_QC result json was written to OceanDNA-b38575/dqc_result.json
[2023-03-18 00:16:32,912] [INFO] DFAST_QC completed!
[2023-03-18 00:16:32,913] [INFO] Total running time: 0h1m24s