[2024-01-24 13:32:13,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:13,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:13,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference
[2024-01-24 13:32:14,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:14,338] [INFO] Task started: Prodigal
[2024-01-24 13:32:14,338] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfb948eb-a6a2-4925-9f00-f57f4449e905/GCF_000813265.1_ASM81326v1_genomic.fna.gz | prodigal -d GCF_000813265.1_ASM81326v1_genomic.fna/cds.fna -a GCF_000813265.1_ASM81326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:30,097] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:30,098] [INFO] Task started: HMMsearch
[2024-01-24 13:32:30,098] [INFO] Running command: hmmsearch --tblout GCF_000813265.1_ASM81326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference/reference_markers.hmm GCF_000813265.1_ASM81326v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:30,367] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:30,368] [INFO] Found 6/6 markers.
[2024-01-24 13:32:30,410] [INFO] Query marker FASTA was written to GCF_000813265.1_ASM81326v1_genomic.fna/markers.fasta
[2024-01-24 13:32:30,411] [INFO] Task started: Blastn
[2024-01-24 13:32:30,411] [INFO] Running command: blastn -query GCF_000813265.1_ASM81326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference/reference_markers.fasta -out GCF_000813265.1_ASM81326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:31,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:31,422] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:31,423] [INFO] Target genome list was writen to GCF_000813265.1_ASM81326v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:31,427] [INFO] Task started: fastANI
[2024-01-24 13:32:31,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb948eb-a6a2-4925-9f00-f57f4449e905/GCF_000813265.1_ASM81326v1_genomic.fna.gz --refList GCF_000813265.1_ASM81326v1_genomic.fna/target_genomes.txt --output GCF_000813265.1_ASM81326v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:49,288] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:49,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:49,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:49,302] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:49,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:49,302] [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 mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	100.0	1695	1696	95	conclusive
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	99.9956	1695	1696	95	conclusive
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	90.5973	1355	1696	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	89.8264	1352	1696	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	89.147	1363	1696	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	89.1324	1363	1696	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	88.9193	1379	1696	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	88.8987	1148	1696	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	88.8937	1383	1696	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	88.8274	1395	1696	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	88.806	1401	1696	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	88.0823	1320	1696	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.0852	942	1696	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.0171	878	1696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,304] [INFO] DFAST Taxonomy check result was written to GCF_000813265.1_ASM81326v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:49,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:49,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:49,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference/checkm_data
[2024-01-24 13:32:49,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:49,355] [INFO] Task started: CheckM
[2024-01-24 13:32:49,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000813265.1_ASM81326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000813265.1_ASM81326v1_genomic.fna/checkm_input GCF_000813265.1_ASM81326v1_genomic.fna/checkm_result
[2024-01-24 13:33:38,617] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:38,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:38,638] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:38,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:38,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000813265.1_ASM81326v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:38,640] [INFO] Task started: Blastn
[2024-01-24 13:33:38,640] [INFO] Running command: blastn -query GCF_000813265.1_ASM81326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg306ed509-f07e-4202-8a4a-48096059d06b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000813265.1_ASM81326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:40,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:40,542] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:40,542] [INFO] Target genome list was writen to GCF_000813265.1_ASM81326v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:40,559] [INFO] Task started: fastANI
[2024-01-24 13:33:40,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb948eb-a6a2-4925-9f00-f57f4449e905/GCF_000813265.1_ASM81326v1_genomic.fna.gz --refList GCF_000813265.1_ASM81326v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000813265.1_ASM81326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:59,917] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:59,933] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:59,933] [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_900636545.1	s__Pseudomonas_E mendocina	99.9956	1695	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	conclusive
GCF_016008875.1	s__Pseudomonas_E sp002439135	91.1985	1384	1696	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_000418555.1	s__Pseudomonas_E sp000418555	90.6875	1406	1696	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_009932725.1	s__Pseudomonas_E sp009932725	90.5973	1355	1696	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_007049795.1	s__Pseudomonas_E mendocina_D	89.9976	1283	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.17	96.47	0.87	0.84	6	-
GCF_900104265.1	s__Pseudomonas_E guguanensis	89.8153	1353	1696	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_002741105.1	s__Pseudomonas_E sediminis	89.4193	1388	1696	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_900106015.1	s__Pseudomonas_E sihuiensis	89.1431	1362	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	89.064	1354	1696	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_002197815.1	s__Pseudomonas_E oleovorans	88.9549	1166	1696	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_900115695.1	s__Pseudomonas_E toyotomiensis	88.9201	1378	1696	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_900115475.1	s__Pseudomonas_E composti	88.8455	1422	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.90	97.79	0.91	0.90	5	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	88.8144	1400	1696	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_001567565.1	s__Pseudomonas_E composti_A	88.5816	1380	1696	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	88.1743	1317	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:59,935] [INFO] GTDB search result was written to GCF_000813265.1_ASM81326v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:59,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:59,940] [INFO] DFAST_QC result json was written to GCF_000813265.1_ASM81326v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:59,940] [INFO] DFAST_QC completed!
[2024-01-24 13:33:59,940] [INFO] Total running time: 0h1m47s