[2024-01-24 11:51:37,001] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,003] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference
[2024-01-24 11:51:38,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,227] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,227] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d9c0502-0ff9-4a37-8563-033c4fe3f1da/GCF_000818015.1_ASM81801v1_genomic.fna.gz | prodigal -d GCF_000818015.1_ASM81801v1_genomic.fna/cds.fna -a GCF_000818015.1_ASM81801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:51,183] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:51,183] [INFO] Task started: HMMsearch
[2024-01-24 11:51:51,183] [INFO] Running command: hmmsearch --tblout GCF_000818015.1_ASM81801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference/reference_markers.hmm GCF_000818015.1_ASM81801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:51,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:51,493] [INFO] Found 6/6 markers.
[2024-01-24 11:51:51,530] [INFO] Query marker FASTA was written to GCF_000818015.1_ASM81801v1_genomic.fna/markers.fasta
[2024-01-24 11:51:51,531] [INFO] Task started: Blastn
[2024-01-24 11:51:51,531] [INFO] Running command: blastn -query GCF_000818015.1_ASM81801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference/reference_markers.fasta -out GCF_000818015.1_ASM81801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:52,533] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:52,537] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:52,537] [INFO] Target genome list was writen to GCF_000818015.1_ASM81801v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:52,545] [INFO] Task started: fastANI
[2024-01-24 11:51:52,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d9c0502-0ff9-4a37-8563-033c4fe3f1da/GCF_000818015.1_ASM81801v1_genomic.fna.gz --refList GCF_000818015.1_ASM81801v1_genomic.fna/target_genomes.txt --output GCF_000818015.1_ASM81801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:07,433] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:07,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:07,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:07,451] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:07,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:07,452] [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
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	100.0	1461	1461	95	conclusive
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	99.9796	1438	1461	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	84.3814	1057	1461	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	84.3724	1071	1461	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	84.2882	1017	1461	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	84.2512	1035	1461	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	84.2302	1010	1461	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	84.2181	1028	1461	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	84.2024	986	1461	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	84.1966	1026	1461	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	83.485	983	1461	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	83.4041	977	1461	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	81.3463	745	1461	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.9829	678	1461	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	80.9326	668	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:07,454] [INFO] DFAST Taxonomy check result was written to GCF_000818015.1_ASM81801v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:07,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:07,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:07,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference/checkm_data
[2024-01-24 11:52:07,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:07,505] [INFO] Task started: CheckM
[2024-01-24 11:52:07,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000818015.1_ASM81801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000818015.1_ASM81801v1_genomic.fna/checkm_input GCF_000818015.1_ASM81801v1_genomic.fna/checkm_result
[2024-01-24 11:52:48,742] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:48,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:48,763] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:48,763] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:48,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000818015.1_ASM81801v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:48,764] [INFO] Task started: Blastn
[2024-01-24 11:52:48,764] [INFO] Running command: blastn -query GCF_000818015.1_ASM81801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88145775-e872-45bb-af87-29907fe401ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_000818015.1_ASM81801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:50,686] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:50,691] [INFO] Selected 15 target genomes.
[2024-01-24 11:52:50,691] [INFO] Target genome list was writen to GCF_000818015.1_ASM81801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:50,706] [INFO] Task started: fastANI
[2024-01-24 11:52:50,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d9c0502-0ff9-4a37-8563-033c4fe3f1da/GCF_000818015.1_ASM81801v1_genomic.fna.gz --refList GCF_000818015.1_ASM81801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000818015.1_ASM81801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:06,074] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:06,090] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:06,090] [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_000818015.1	s__Pseudomonas_A balearica	100.0	1460	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.54	98.20	0.91	0.86	18	conclusive
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	84.4814	1044	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	84.3867	1056	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	84.2153	1008	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	84.1305	969	1461	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_005844005.1	s__Pseudomonas_A sp000765155	84.0866	996	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	84.039	1000	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	83.7808	1023	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	83.5796	985	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	83.3955	978	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	83.3774	936	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	82.531	895	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	81.3359	747	1461	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_003595175.1	s__Pseudomonas_E sp003595175	80.9767	680	1461	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_014490745.1	s__Pseudomonas_E alcaligenes_C	80.9666	700	1461	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 11:53:06,092] [INFO] GTDB search result was written to GCF_000818015.1_ASM81801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:06,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:06,096] [INFO] DFAST_QC result json was written to GCF_000818015.1_ASM81801v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:06,096] [INFO] DFAST_QC completed!
[2024-01-24 11:53:06,096] [INFO] Total running time: 0h1m29s