[2023-03-16 05:21:40,849] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:21:40,852] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:21:40,852] [INFO] DQC Reference Directory: /var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference
[2023-03-16 05:21:42,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:21:42,001] [INFO] Task started: Prodigal
[2023-03-16 05:21:42,001] [INFO] Running command: cat /var/lib/cwl/stg1c5f63e9-d261-4bda-857f-4d87081ea311/OceanDNA-b38572.fa | prodigal -d OceanDNA-b38572/cds.fna -a OceanDNA-b38572/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:21:56,031] [INFO] Task succeeded: Prodigal
[2023-03-16 05:21:56,031] [INFO] Task started: HMMsearch
[2023-03-16 05:21:56,031] [INFO] Running command: hmmsearch --tblout OceanDNA-b38572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference/reference_markers.hmm OceanDNA-b38572/protein.faa > /dev/null
[2023-03-16 05:21:56,245] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:21:56,245] [INFO] Found 6/6 markers.
[2023-03-16 05:21:56,325] [INFO] Query marker FASTA was written to OceanDNA-b38572/markers.fasta
[2023-03-16 05:21:56,327] [INFO] Task started: Blastn
[2023-03-16 05:21:56,327] [INFO] Running command: blastn -query OceanDNA-b38572/markers.fasta -db /var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference/reference_markers.fasta -out OceanDNA-b38572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:21:57,002] [INFO] Task succeeded: Blastn
[2023-03-16 05:21:57,025] [INFO] Selected 17 target genomes.
[2023-03-16 05:21:57,025] [INFO] Target genome list was writen to OceanDNA-b38572/target_genomes.txt
[2023-03-16 05:21:57,033] [INFO] Task started: fastANI
[2023-03-16 05:21:57,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5f63e9-d261-4bda-857f-4d87081ea311/OceanDNA-b38572.fa --refList OceanDNA-b38572/target_genomes.txt --output OceanDNA-b38572/fastani_result.tsv --threads 1
[2023-03-16 05:22:08,362] [INFO] Task succeeded: fastANI
[2023-03-16 05:22:08,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:22:08,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:22:08,380] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 05:22:08,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 05:22:08,380] [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 junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	98.0597	793	849	95	conclusive
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	98.0251	792	849	95	conclusive
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	83.9713	505	849	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	83.9052	521	849	95	below_threshold
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	83.8574	599	849	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	83.8198	589	849	95	below_threshold
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	83.7415	565	849	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	83.719	604	849	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.6305	625	849	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	83.6287	640	849	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	82.8821	566	849	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	82.8207	574	849	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	82.6129	581	849	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	82.5388	592	849	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.3009	415	849	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.1237	397	849	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.1102	403	849	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:22:08,390] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38572/tc_result.tsv
[2023-03-16 05:22:08,406] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:22:08,406] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:22:08,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference/checkm_data
[2023-03-16 05:22:08,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:22:08,420] [INFO] Task started: CheckM
[2023-03-16 05:22:08,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38572/checkm_input OceanDNA-b38572/checkm_result
[2023-03-16 05:22:47,237] [INFO] Task succeeded: CheckM
[2023-03-16 05:22:47,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:22:47,365] [INFO] ===== Completeness check finished =====
[2023-03-16 05:22:47,365] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:22:47,365] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38572/markers.fasta)
[2023-03-16 05:22:47,366] [INFO] Task started: Blastn
[2023-03-16 05:22:47,367] [INFO] Running command: blastn -query OceanDNA-b38572/markers.fasta -db /var/lib/cwl/stg03b30861-3681-4804-9066-c5d628e57214/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:22:48,545] [INFO] Task succeeded: Blastn
[2023-03-16 05:22:48,575] [INFO] Selected 16 target genomes.
[2023-03-16 05:22:48,575] [INFO] Target genome list was writen to OceanDNA-b38572/target_genomes_gtdb.txt
[2023-03-16 05:22:48,587] [INFO] Task started: fastANI
[2023-03-16 05:22:48,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c5f63e9-d261-4bda-857f-4d87081ea311/OceanDNA-b38572.fa --refList OceanDNA-b38572/target_genomes_gtdb.txt --output OceanDNA-b38572/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:22:59,862] [INFO] Task succeeded: fastANI
[2023-03-16 05:22:59,871] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:22:59,871] [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_000368765.1	s__Acinetobacter junii	98.0251	792	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	85.3764	572	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000369005.1	s__Acinetobacter beijerinckii	84.932	655	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_014636095.1	s__Acinetobacter modestus	84.0974	596	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_000368025.1	s__Acinetobacter parvus	83.9029	522	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
GCF_000369065.1	s__Acinetobacter haemolyticus	83.7996	591	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
GCF_000368585.1	s__Acinetobacter venetianus	83.6679	637	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCA_003987695.1	s__Acinetobacter sp003987695	83.194	565	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000374425.1	s__Acinetobacter tjernbergiae	83.1022	615	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCF_000367945.1	s__Acinetobacter proteolyticus	82.8385	572	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000369525.1	s__Acinetobacter sp000369525	82.8116	594	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_011753255.1	s__Acinetobacter sp011753255	82.7365	586	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400715.1	s__Acinetobacter sp000400715	82.706	603	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	82.6225	580	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_014635885.1	s__Acinetobacter vivianii	82.5579	562	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000368825.1	s__Acinetobacter ursingii	79.9546	305	849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	-
--------------------------------------------------------------------------------
[2023-03-16 05:22:59,882] [INFO] GTDB search result was written to OceanDNA-b38572/result_gtdb.tsv
[2023-03-16 05:22:59,903] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:22:59,920] [INFO] DFAST_QC result json was written to OceanDNA-b38572/dqc_result.json
[2023-03-16 05:22:59,920] [INFO] DFAST_QC completed!
[2023-03-16 05:22:59,920] [INFO] Total running time: 0h1m19s