[2023-06-29 01:46:48,291] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:46:48,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:46:48,293] [INFO] DQC Reference Directory: /var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference
[2023-06-29 01:46:50,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:46:50,678] [INFO] Task started: Prodigal
[2023-06-29 01:46:50,678] [INFO] Running command: gunzip -c /var/lib/cwl/stge431202a-281f-4478-aa07-98650440e71c/GCA_027441795.1_ASM2744179v1_genomic.fna.gz | prodigal -d GCA_027441795.1_ASM2744179v1_genomic.fna/cds.fna -a GCA_027441795.1_ASM2744179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:46:55,590] [INFO] Task succeeded: Prodigal
[2023-06-29 01:46:55,590] [INFO] Task started: HMMsearch
[2023-06-29 01:46:55,591] [INFO] Running command: hmmsearch --tblout GCA_027441795.1_ASM2744179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference/reference_markers.hmm GCA_027441795.1_ASM2744179v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:46:55,762] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:46:55,763] [INFO] Found 6/6 markers.
[2023-06-29 01:46:55,784] [INFO] Query marker FASTA was written to GCA_027441795.1_ASM2744179v1_genomic.fna/markers.fasta
[2023-06-29 01:46:55,785] [INFO] Task started: Blastn
[2023-06-29 01:46:55,785] [INFO] Running command: blastn -query GCA_027441795.1_ASM2744179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference/reference_markers.fasta -out GCA_027441795.1_ASM2744179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:46:56,525] [INFO] Task succeeded: Blastn
[2023-06-29 01:46:56,528] [INFO] Selected 34 target genomes.
[2023-06-29 01:46:56,528] [INFO] Target genome list was writen to GCA_027441795.1_ASM2744179v1_genomic.fna/target_genomes.txt
[2023-06-29 01:46:56,533] [INFO] Task started: fastANI
[2023-06-29 01:46:56,533] [INFO] Running command: fastANI --query /var/lib/cwl/stge431202a-281f-4478-aa07-98650440e71c/GCA_027441795.1_ASM2744179v1_genomic.fna.gz --refList GCA_027441795.1_ASM2744179v1_genomic.fna/target_genomes.txt --output GCA_027441795.1_ASM2744179v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:47:16,470] [INFO] Task succeeded: fastANI
[2023-06-29 01:47:16,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:47:16,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:47:16,484] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:47:16,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 01:47:16,484] [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 oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.3337	65	495	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.2412	65	495	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	76.2026	62	495	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.1993	57	495	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	75.9853	69	495	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	75.9643	70	495	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.8691	81	495	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	75.8466	58	495	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	75.8461	67	495	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	75.8278	58	495	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	75.8261	68	495	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.8191	66	495	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.8183	66	495	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.8183	66	495	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	75.7373	61	495	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 01:47:16,486] [INFO] DFAST Taxonomy check result was written to GCA_027441795.1_ASM2744179v1_genomic.fna/tc_result.tsv
[2023-06-29 01:47:16,486] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:47:16,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:47:16,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference/checkm_data
[2023-06-29 01:47:16,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:47:16,510] [INFO] Task started: CheckM
[2023-06-29 01:47:16,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027441795.1_ASM2744179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027441795.1_ASM2744179v1_genomic.fna/checkm_input GCA_027441795.1_ASM2744179v1_genomic.fna/checkm_result
[2023-06-29 01:47:37,199] [INFO] Task succeeded: CheckM
[2023-06-29 01:47:37,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:47:37,217] [INFO] ===== Completeness check finished =====
[2023-06-29 01:47:37,218] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:47:37,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027441795.1_ASM2744179v1_genomic.fna/markers.fasta)
[2023-06-29 01:47:37,218] [INFO] Task started: Blastn
[2023-06-29 01:47:37,218] [INFO] Running command: blastn -query GCA_027441795.1_ASM2744179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab0958e3-e859-49b6-ae59-0e1e62c5a2e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_027441795.1_ASM2744179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:47:38,541] [INFO] Task succeeded: Blastn
[2023-06-29 01:47:38,545] [INFO] Selected 30 target genomes.
[2023-06-29 01:47:38,546] [INFO] Target genome list was writen to GCA_027441795.1_ASM2744179v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:47:38,561] [INFO] Task started: fastANI
[2023-06-29 01:47:38,561] [INFO] Running command: fastANI --query /var/lib/cwl/stge431202a-281f-4478-aa07-98650440e71c/GCA_027441795.1_ASM2744179v1_genomic.fna.gz --refList GCA_027441795.1_ASM2744179v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027441795.1_ASM2744179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:47:54,333] [INFO] Task succeeded: fastANI
[2023-06-29 01:47:54,344] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 01:47:54,344] [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_002943415.1	s__Perlucidibaca sp002943415	77.0087	87	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	76.6671	59	495	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_000420045.1	s__Perlucidibaca piscinae	76.5972	84	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	76.3057	66	495	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_004801855.1	s__Pseudomonas_K sp004801855	76.2929	70	495	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_900112375.1	s__Pseudomonas citronellolis	76.1439	76	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	76.1108	69	495	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_900156545.1	s__Pseudomonas_E alcaligenes_A	75.9934	61	495	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_004327355.1	s__Pseudomonas_E dryadis	75.8855	63	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	75.8463	60	495	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_000467105.1	s__Pseudomonas_E alcaligenes	75.8461	67	495	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_000474945.1	s__Solimonas soli	75.8037	59	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015637705.1	s__Pseudomonas_E sp015637705	75.7634	51	495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 01:47:54,346] [INFO] GTDB search result was written to GCA_027441795.1_ASM2744179v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:47:54,346] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:47:54,350] [INFO] DFAST_QC result json was written to GCA_027441795.1_ASM2744179v1_genomic.fna/dqc_result.json
[2023-06-29 01:47:54,350] [INFO] DFAST_QC completed!
[2023-06-29 01:47:54,350] [INFO] Total running time: 0h1m6s