[2024-01-24 13:40:28,742] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,744] [INFO] DQC Reference Directory: /var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference
[2024-01-24 13:40:30,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:30,156] [INFO] Task started: Prodigal
[2024-01-24 13:40:30,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d037f0f-f73b-4aa2-b241-69ab51e6c987/GCF_002943415.1_ASM294341v1_genomic.fna.gz | prodigal -d GCF_002943415.1_ASM294341v1_genomic.fna/cds.fna -a GCF_002943415.1_ASM294341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:34,838] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:34,838] [INFO] Task started: HMMsearch
[2024-01-24 13:40:34,838] [INFO] Running command: hmmsearch --tblout GCF_002943415.1_ASM294341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference/reference_markers.hmm GCF_002943415.1_ASM294341v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:35,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:35,025] [INFO] Found 6/6 markers.
[2024-01-24 13:40:35,049] [INFO] Query marker FASTA was written to GCF_002943415.1_ASM294341v1_genomic.fna/markers.fasta
[2024-01-24 13:40:35,050] [INFO] Task started: Blastn
[2024-01-24 13:40:35,050] [INFO] Running command: blastn -query GCF_002943415.1_ASM294341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference/reference_markers.fasta -out GCF_002943415.1_ASM294341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:36,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:36,145] [INFO] Selected 27 target genomes.
[2024-01-24 13:40:36,145] [INFO] Target genome list was writen to GCF_002943415.1_ASM294341v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:36,162] [INFO] Task started: fastANI
[2024-01-24 13:40:36,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d037f0f-f73b-4aa2-b241-69ab51e6c987/GCF_002943415.1_ASM294341v1_genomic.fna.gz --refList GCF_002943415.1_ASM294341v1_genomic.fna/target_genomes.txt --output GCF_002943415.1_ASM294341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:58,260] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:58,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:58,281] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:58,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:58,281] [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
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	79.239	267	436	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	79.1807	251	436	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	79.1642	268	436	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	79.1385	257	436	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	79.0152	235	436	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.8913	225	436	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	78.8145	210	436	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.7829	224	436	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.7341	243	436	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.6279	210	436	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	78.6203	231	436	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	78.6008	209	436	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	78.5899	232	436	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	78.5894	209	436	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	78.5793	217	436	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	78.4992	198	436	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.3113	221	436	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	78.2295	233	436	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	78.135	175	436	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_003850565.1	658629	658629	type	True	78.0409	123	436	95	below_threshold
Pseudomonas farsensis	strain=SWRI107	GCA_014268805.2	2745492	2745492	type	True	78.0322	132	436	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.0186	204	436	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.0093	202	436	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	77.9745	218	436	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_019139855.1	658629	658629	type	True	77.9263	121	436	95	below_threshold
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	77.5205	107	436	95	below_threshold
Paraperlucidibaca baekdonensis	strain=DSM 26022	GCA_003387535.1	748120	748120	type	True	77.2894	146	436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,283] [INFO] DFAST Taxonomy check result was written to GCF_002943415.1_ASM294341v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:58,284] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:58,284] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:58,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference/checkm_data
[2024-01-24 13:40:58,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:58,308] [INFO] Task started: CheckM
[2024-01-24 13:40:58,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002943415.1_ASM294341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002943415.1_ASM294341v1_genomic.fna/checkm_input GCF_002943415.1_ASM294341v1_genomic.fna/checkm_result
[2024-01-24 13:41:19,022] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:19,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:19,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:19,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002943415.1_ASM294341v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:19,040] [INFO] Task started: Blastn
[2024-01-24 13:41:19,040] [INFO] Running command: blastn -query GCF_002943415.1_ASM294341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd78d1e3b-e099-4759-8aaa-a70668c9974d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002943415.1_ASM294341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:21,131] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:21,134] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:21,134] [INFO] Target genome list was writen to GCF_002943415.1_ASM294341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:21,146] [INFO] Task started: fastANI
[2024-01-24 13:41:21,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d037f0f-f73b-4aa2-b241-69ab51e6c987/GCF_002943415.1_ASM294341v1_genomic.fna.gz --refList GCF_002943415.1_ASM294341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002943415.1_ASM294341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:34,640] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:34,656] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:34,657] [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_002943415.1	s__Perlucidibaca sp002943415	100.0	425	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420045.1	s__Perlucidibaca piscinae	84.4509	398	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676655.1	s__Perlucidibaca aquatica	79.7207	200	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	79.2646	265	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCA_002342025.1	s__Perlucidibaca sp002342025	79.2393	145	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112375.1	s__Pseudomonas citronellolis	79.1523	253	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	79.0346	234	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	78.8515	231	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	78.8145	210	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_900104805.1	s__Pseudomonas_K oryzae	78.7674	241	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	78.6582	223	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	78.5913	232	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_004339665.1	s__Azotobacter chroococcum	78.5732	211	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_900110885.1	s__Azotobacter beijerinckii	78.477	199	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	78.35	198	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111835.1	s__Pseudomonas_F otitidis	78.2626	231	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
GCF_009363155.1	s__Azotobacter salinestris	78.2288	206	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418465.1	s__Pseudomonas_O sp002418465	78.1016	194	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003543245.1	s__UBA2031 sp003543245	77.9736	139	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__UBA2031	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387535.1	s__Paraperlucidibaca baekdonensis	77.2894	146	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Paraperlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:34,659] [INFO] GTDB search result was written to GCF_002943415.1_ASM294341v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:34,659] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:34,664] [INFO] DFAST_QC result json was written to GCF_002943415.1_ASM294341v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:34,664] [INFO] DFAST_QC completed!
[2024-01-24 13:41:34,664] [INFO] Total running time: 0h1m6s