[2024-01-24 15:14:52,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference
[2024-01-24 15:14:53,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,691] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c88d825-7844-44e6-865f-9c154091263f/GCF_003864255.1_ASM386425v1_genomic.fna.gz | prodigal -d GCF_003864255.1_ASM386425v1_genomic.fna/cds.fna -a GCF_003864255.1_ASM386425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:04,349] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:04,350] [INFO] Task started: HMMsearch
[2024-01-24 15:15:04,350] [INFO] Running command: hmmsearch --tblout GCF_003864255.1_ASM386425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference/reference_markers.hmm GCF_003864255.1_ASM386425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:04,643] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:04,644] [INFO] Found 6/6 markers.
[2024-01-24 15:15:04,677] [INFO] Query marker FASTA was written to GCF_003864255.1_ASM386425v1_genomic.fna/markers.fasta
[2024-01-24 15:15:04,677] [INFO] Task started: Blastn
[2024-01-24 15:15:04,677] [INFO] Running command: blastn -query GCF_003864255.1_ASM386425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference/reference_markers.fasta -out GCF_003864255.1_ASM386425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:05,563] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:05,573] [INFO] Selected 28 target genomes.
[2024-01-24 15:15:05,573] [INFO] Target genome list was writen to GCF_003864255.1_ASM386425v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:05,586] [INFO] Task started: fastANI
[2024-01-24 15:15:05,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c88d825-7844-44e6-865f-9c154091263f/GCF_003864255.1_ASM386425v1_genomic.fna.gz --refList GCF_003864255.1_ASM386425v1_genomic.fna/target_genomes.txt --output GCF_003864255.1_ASM386425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:25,996] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:25,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:25,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:26,024] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:15:26,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:26,024] [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
Aestuariirhabdus litorea	strain=GTF13	GCA_003864255.1	2528527	2528527	type	True	100.0	1218	1218	95	conclusive
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	76.9692	173	1218	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.943	115	1218	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9374	189	1218	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	76.896	151	1218	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	76.8442	160	1218	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.8311	120	1218	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.8211	187	1218	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	76.7656	120	1218	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	76.7595	136	1218	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.7434	179	1218	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	76.7393	139	1218	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.7356	118	1218	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.7278	155	1218	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	76.7218	135	1218	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	76.6987	120	1218	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	76.6968	190	1218	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	76.6944	122	1218	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	76.6563	156	1218	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	76.6561	168	1218	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.6405	192	1218	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.6228	142	1218	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.5362	134	1218	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.5145	163	1218	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	76.4935	88	1218	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.481	173	1218	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	76.3049	90	1218	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	76.2491	102	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:26,026] [INFO] DFAST Taxonomy check result was written to GCF_003864255.1_ASM386425v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:26,027] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:26,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:26,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference/checkm_data
[2024-01-24 15:15:26,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:26,065] [INFO] Task started: CheckM
[2024-01-24 15:15:26,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003864255.1_ASM386425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003864255.1_ASM386425v1_genomic.fna/checkm_input GCF_003864255.1_ASM386425v1_genomic.fna/checkm_result
[2024-01-24 15:16:00,312] [INFO] Task succeeded: CheckM
[2024-01-24 15:16:00,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:16:00,335] [INFO] ===== Completeness check finished =====
[2024-01-24 15:16:00,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:16:00,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003864255.1_ASM386425v1_genomic.fna/markers.fasta)
[2024-01-24 15:16:00,337] [INFO] Task started: Blastn
[2024-01-24 15:16:00,337] [INFO] Running command: blastn -query GCF_003864255.1_ASM386425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdfde9b-1efe-4813-9562-3ac721641778/dqc_reference/reference_markers_gtdb.fasta -out GCF_003864255.1_ASM386425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:16:01,759] [INFO] Task succeeded: Blastn
[2024-01-24 15:16:01,763] [INFO] Selected 26 target genomes.
[2024-01-24 15:16:01,764] [INFO] Target genome list was writen to GCF_003864255.1_ASM386425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:16:01,786] [INFO] Task started: fastANI
[2024-01-24 15:16:01,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c88d825-7844-44e6-865f-9c154091263f/GCF_003864255.1_ASM386425v1_genomic.fna.gz --refList GCF_003864255.1_ASM386425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003864255.1_ASM386425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:16:20,273] [INFO] Task succeeded: fastANI
[2024-01-24 15:16:20,295] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:16:20,295] [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_003864255.1	s__Aestuariirhabdus litorea	100.0	1218	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Aestuariirhabdaceae;g__Aestuariirhabdus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018398425.1	s__Pseudomonas_E lalucatii	76.9599	187	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	76.9434	173	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.8889	172	1218	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_904061905.1	s__Pseudomonas_E carbonaria	76.8451	162	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	76.7624	160	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877905.1	s__Pseudomonas nicosulfuronedens	76.7595	136	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	76.7358	120	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.7315	178	1218	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_900115175.1	s__Marinobacter gudaonensis	76.6956	111	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	76.6855	121	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	76.6803	136	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	76.6489	161	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187505.1	s__Pseudomonas_E sp900187505	76.5831	85	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.03	0.87	0.86	4	-
GCF_000761545.1	s__Pseudomonas_E sp000761545	76.5798	150	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858275.1	s__Pseudomonas_E proteolytica	76.5045	90	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	76.5042	87	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.5001	180	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_000313755.1	s__Pseudomonas nitroreducens_A	76.486	150	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	96.60	96.60	0.86	0.86	2	-
GCF_004327335.1	s__Pseudomonas_Q kirkiae	76.4688	138	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	99.65	99.41	0.96	0.94	4	-
GCF_016925675.1	s__Pseudomonas_E sp012985665	76.334	104	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	97.44	0.92	0.88	4	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	76.3078	144	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646575.1	s__Pseudomonas_D pertucinogena	76.2535	129	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	76.2491	102	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_900105185.1	s__Pseudomonas_E saponiphila	76.2432	125	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
GCA_014762755.1	s__Marinobacter sp014762755	76.0162	69	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:16:20,297] [INFO] GTDB search result was written to GCF_003864255.1_ASM386425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:16:20,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:16:20,303] [INFO] DFAST_QC result json was written to GCF_003864255.1_ASM386425v1_genomic.fna/dqc_result.json
[2024-01-24 15:16:20,303] [INFO] DFAST_QC completed!
[2024-01-24 15:16:20,303] [INFO] Total running time: 0h1m28s