[2024-01-24 15:01:14,991] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,993] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,993] [INFO] DQC Reference Directory: /var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference
[2024-01-24 15:01:16,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:16,183] [INFO] Task started: Prodigal
[2024-01-24 15:01:16,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg51b02bc6-0b8d-4e69-aace-e0f877a6d7ff/GCF_002234375.1_ASM223437v1_genomic.fna.gz | prodigal -d GCF_002234375.1_ASM223437v1_genomic.fna/cds.fna -a GCF_002234375.1_ASM223437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:26,154] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:26,155] [INFO] Task started: HMMsearch
[2024-01-24 15:01:26,155] [INFO] Running command: hmmsearch --tblout GCF_002234375.1_ASM223437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference/reference_markers.hmm GCF_002234375.1_ASM223437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:26,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:26,409] [INFO] Found 6/6 markers.
[2024-01-24 15:01:26,439] [INFO] Query marker FASTA was written to GCF_002234375.1_ASM223437v1_genomic.fna/markers.fasta
[2024-01-24 15:01:26,440] [INFO] Task started: Blastn
[2024-01-24 15:01:26,440] [INFO] Running command: blastn -query GCF_002234375.1_ASM223437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference/reference_markers.fasta -out GCF_002234375.1_ASM223437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:27,441] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:27,446] [INFO] Selected 20 target genomes.
[2024-01-24 15:01:27,446] [INFO] Target genome list was writen to GCF_002234375.1_ASM223437v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:27,502] [INFO] Task started: fastANI
[2024-01-24 15:01:27,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg51b02bc6-0b8d-4e69-aace-e0f877a6d7ff/GCF_002234375.1_ASM223437v1_genomic.fna.gz --refList GCF_002234375.1_ASM223437v1_genomic.fna/target_genomes.txt --output GCF_002234375.1_ASM223437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:44,411] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:44,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:44,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:44,432] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:01:44,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:44,432] [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 fluvialis	strain=ASS-1	GCA_002234375.1	1793966	1793966	suspected-type	True	100.0	1066	1068	95	conclusive
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	99.9874	1067	1068	95	conclusive
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	82.5528	665	1068	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	82.5372	659	1068	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.8093	648	1068	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.6017	655	1068	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	81.5201	616	1068	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	81.5101	645	1068	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.4347	625	1068	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.4324	529	1068	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.4129	581	1068	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	81.2142	602	1068	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.1502	574	1068	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	81.0924	615	1068	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	80.9824	595	1068	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	80.9259	558	1068	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	80.9242	590	1068	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	80.8446	554	1068	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	80.7339	567	1068	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	80.4871	509	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:44,434] [INFO] DFAST Taxonomy check result was written to GCF_002234375.1_ASM223437v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:44,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:44,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:44,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference/checkm_data
[2024-01-24 15:01:44,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:44,470] [INFO] Task started: CheckM
[2024-01-24 15:01:44,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002234375.1_ASM223437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002234375.1_ASM223437v1_genomic.fna/checkm_input GCF_002234375.1_ASM223437v1_genomic.fna/checkm_result
[2024-01-24 15:02:17,067] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:17,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:17,089] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:17,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:17,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002234375.1_ASM223437v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:17,090] [INFO] Task started: Blastn
[2024-01-24 15:02:17,090] [INFO] Running command: blastn -query GCF_002234375.1_ASM223437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga663d364-92ce-46db-aded-65c47697a948/dqc_reference/reference_markers_gtdb.fasta -out GCF_002234375.1_ASM223437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:19,017] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:19,020] [INFO] Selected 18 target genomes.
[2024-01-24 15:02:19,020] [INFO] Target genome list was writen to GCF_002234375.1_ASM223437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:19,040] [INFO] Task started: fastANI
[2024-01-24 15:02:19,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg51b02bc6-0b8d-4e69-aace-e0f877a6d7ff/GCF_002234375.1_ASM223437v1_genomic.fna.gz --refList GCF_002234375.1_ASM223437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002234375.1_ASM223437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:34,337] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:34,352] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:34,353] [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_002234375.1	s__Pseudomonas_E fluvialis	100.0	1066	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	98.53	0.96	0.92	3	conclusive
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	82.5762	649	1068	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_000467105.1	s__Pseudomonas_E alcaligenes	82.4963	662	1068	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_900156545.1	s__Pseudomonas_E alcaligenes_A	82.2991	635	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	81.9755	645	1068	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_003696305.1	s__Pseudomonas_E sp003696305	81.8846	676	1068	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	81.839	648	1068	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_001592875.1	s__Pseudomonas_E sp001592875	81.8144	622	1068	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_014851565.1	s__Pseudomonas_E sp014851565	81.6829	616	1068	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_900104265.1	s__Pseudomonas_E guguanensis	81.6125	654	1068	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_013200955.2	s__Pseudomonas_E campi	81.5453	642	1068	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_000418555.1	s__Pseudomonas_E sp000418555	81.4884	628	1068	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_004521985.1	s__Pseudomonas_E khazarica	81.4629	636	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCA_002483005.1	s__Pseudomonas_E sp002483005	81.3329	390	1068	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_004801855.1	s__Pseudomonas_K sp004801855	81.2293	518	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900099785.1	s__Pseudomonas panipatensis	80.8907	563	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802425.1	s__Pseudomonas_H flexibilis	80.8317	554	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	99.07	98.74	0.94	0.90	5	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	80.5434	546	1068	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:34,355] [INFO] GTDB search result was written to GCF_002234375.1_ASM223437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:34,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:34,360] [INFO] DFAST_QC result json was written to GCF_002234375.1_ASM223437v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:34,361] [INFO] DFAST_QC completed!
[2024-01-24 15:02:34,361] [INFO] Total running time: 0h1m19s