[2024-01-24 11:26:54,318] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,223] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg072751b3-b76e-4bdb-ac9b-2d3180130eef/GCF_021029445.1_ASM2102944v1_genomic.fna.gz | prodigal -d GCF_021029445.1_ASM2102944v1_genomic.fna/cds.fna -a GCF_021029445.1_ASM2102944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:12,031] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:12,032] [INFO] Task started: HMMsearch
[2024-01-24 11:27:12,032] [INFO] Running command: hmmsearch --tblout GCF_021029445.1_ASM2102944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference/reference_markers.hmm GCF_021029445.1_ASM2102944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:12,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:12,323] [INFO] Found 6/6 markers.
[2024-01-24 11:27:12,365] [INFO] Query marker FASTA was written to GCF_021029445.1_ASM2102944v1_genomic.fna/markers.fasta
[2024-01-24 11:27:12,366] [INFO] Task started: Blastn
[2024-01-24 11:27:12,366] [INFO] Running command: blastn -query GCF_021029445.1_ASM2102944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference/reference_markers.fasta -out GCF_021029445.1_ASM2102944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:13,408] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:13,412] [INFO] Selected 19 target genomes.
[2024-01-24 11:27:13,412] [INFO] Target genome list was writen to GCF_021029445.1_ASM2102944v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:13,432] [INFO] Task started: fastANI
[2024-01-24 11:27:13,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg072751b3-b76e-4bdb-ac9b-2d3180130eef/GCF_021029445.1_ASM2102944v1_genomic.fna.gz --refList GCF_021029445.1_ASM2102944v1_genomic.fna/target_genomes.txt --output GCF_021029445.1_ASM2102944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:35,260] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:35,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:35,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:35,279] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:35,280] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:35,280] [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 oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	91.2166	1121	1484	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	91.1814	1167	1484	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	91.1195	1121	1484	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	90.0169	1191	1484	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	89.8683	1172	1484	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	89.8233	1167	1484	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	89.8227	1182	1484	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	89.4738	1173	1484	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	89.4549	1183	1484	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	89.1565	1156	1484	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	88.9554	1175	1484	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	88.9311	1167	1484	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	88.8204	1161	1484	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	88.7084	1158	1484	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	88.6178	1162	1484	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	88.566	1120	1484	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	88.1923	1162	1484	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.507	898	1484	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.9927	819	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,282] [INFO] DFAST Taxonomy check result was written to GCF_021029445.1_ASM2102944v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:35,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:35,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:35,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference/checkm_data
[2024-01-24 11:27:35,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:35,325] [INFO] Task started: CheckM
[2024-01-24 11:27:35,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021029445.1_ASM2102944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021029445.1_ASM2102944v1_genomic.fna/checkm_input GCF_021029445.1_ASM2102944v1_genomic.fna/checkm_result
[2024-01-24 11:28:17,027] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:17,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:17,055] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:17,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:17,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021029445.1_ASM2102944v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:17,057] [INFO] Task started: Blastn
[2024-01-24 11:28:17,057] [INFO] Running command: blastn -query GCF_021029445.1_ASM2102944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg958f830e-a14a-433c-b10d-e72e756bf068/dqc_reference/reference_markers_gtdb.fasta -out GCF_021029445.1_ASM2102944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:18,984] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:18,987] [INFO] Selected 18 target genomes.
[2024-01-24 11:28:18,987] [INFO] Target genome list was writen to GCF_021029445.1_ASM2102944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:19,003] [INFO] Task started: fastANI
[2024-01-24 11:28:19,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg072751b3-b76e-4bdb-ac9b-2d3180130eef/GCF_021029445.1_ASM2102944v1_genomic.fna.gz --refList GCF_021029445.1_ASM2102944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021029445.1_ASM2102944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:40,327] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:40,345] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:40,346] [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_008041835.1	s__Pseudomonas_E sp002282595	94.2482	1117	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_002197815.1	s__Pseudomonas_E oleovorans	91.1196	1121	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	97.92	96.68	0.87	0.80	18	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	90.9101	1110	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	N/A	N/A	N/A	N/A	1	-
GCF_900102635.1	s__Pseudomonas_E chengduensis	89.8757	1170	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	-
GCF_001941865.1	s__Pseudomonas_E alcaliphila_B	89.7444	1210	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	-
GCF_015712065.1	s__Pseudomonas_E chengduensis_A	89.5575	1184	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7107	97.25	97.17	0.91	0.89	9	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	89.5059	1193	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_900115695.1	s__Pseudomonas_E toyotomiensis	89.4709	1174	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.1942	98.17	97.23	0.91	0.85	7	-
GCF_900104265.1	s__Pseudomonas_E guguanensis	89.178	1155	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	88.925	1167	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_902506495.1	s__Pseudomonas_E sp902506495	88.8776	1182	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.72	95.94	0.90	0.87	3	-
GCF_002741105.1	s__Pseudomonas_E sediminis	88.8059	1162	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.51	0.89	0.85	6	-
GCF_900636545.1	s__Pseudomonas_E mendocina	88.7161	1158	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
GCF_009932725.1	s__Pseudomonas_E sp009932725	88.54	1122	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	88.4768	1113	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_001567565.1	s__Pseudomonas_E composti_A	88.3087	1146	1484	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_000016565.1	s__Pseudomonas_E mendocina_A	88.2991	1146	1484	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_003008615.1	s__Pseudomonas_E mendocina_C	87.2179	1146	1484	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:40,347] [INFO] GTDB search result was written to GCF_021029445.1_ASM2102944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:40,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:40,352] [INFO] DFAST_QC result json was written to GCF_021029445.1_ASM2102944v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:40,352] [INFO] DFAST_QC completed!
[2024-01-24 11:28:40,352] [INFO] Total running time: 0h1m46s