[2024-01-24 13:17:05,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference
[2024-01-24 13:17:06,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,881] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,882] [INFO] Running command: gunzip -c /var/lib/cwl/stga16f8fc9-de62-439f-bb73-3d7765e024fd/GCF_000280765.1_ASM28076v1_genomic.fna.gz | prodigal -d GCF_000280765.1_ASM28076v1_genomic.fna/cds.fna -a GCF_000280765.1_ASM28076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:31,754] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:31,755] [INFO] Task started: HMMsearch
[2024-01-24 13:17:31,755] [INFO] Running command: hmmsearch --tblout GCF_000280765.1_ASM28076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference/reference_markers.hmm GCF_000280765.1_ASM28076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:32,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:32,216] [INFO] Found 6/6 markers.
[2024-01-24 13:17:32,281] [INFO] Query marker FASTA was written to GCF_000280765.1_ASM28076v1_genomic.fna/markers.fasta
[2024-01-24 13:17:32,281] [INFO] Task started: Blastn
[2024-01-24 13:17:32,281] [INFO] Running command: blastn -query GCF_000280765.1_ASM28076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference/reference_markers.fasta -out GCF_000280765.1_ASM28076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:33,409] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:33,417] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:33,417] [INFO] Target genome list was writen to GCF_000280765.1_ASM28076v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:33,423] [INFO] Task started: fastANI
[2024-01-24 13:17:33,423] [INFO] Running command: fastANI --query /var/lib/cwl/stga16f8fc9-de62-439f-bb73-3d7765e024fd/GCF_000280765.1_ASM28076v1_genomic.fna.gz --refList GCF_000280765.1_ASM28076v1_genomic.fna/target_genomes.txt --output GCF_000280765.1_ASM28076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:51,563] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:51,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:51,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:51,575] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:51,575] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:51,575] [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 agarici	strain=LMG 2112	GCA_900109755.1	46677	46677	type	True	88.7379	1336	2524	95	below_threshold
Pseudomonas agarici	strain=IPO3740	GCA_013385305.1	46677	46677	type	True	88.709	1342	2524	95	below_threshold
Pseudomonas agarici	strain=NCPPB 2289	GCA_000280785.1	46677	46677	type	True	88.5868	1361	2524	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	87.0104	1483	2524	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	86.9877	1584	2524	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	84.9209	1436	2524	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	83.2389	1302	2524	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.5291	1014	2524	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	82.4522	1124	2524	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.4424	1067	2524	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.8756	1031	2524	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	81.8468	1005	2524	95	below_threshold
Pseudomonas baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	81.7094	832	2524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:51,577] [INFO] DFAST Taxonomy check result was written to GCF_000280765.1_ASM28076v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:51,578] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:51,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:51,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference/checkm_data
[2024-01-24 13:17:51,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:51,653] [INFO] Task started: CheckM
[2024-01-24 13:17:51,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000280765.1_ASM28076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000280765.1_ASM28076v1_genomic.fna/checkm_input GCF_000280765.1_ASM28076v1_genomic.fna/checkm_result
[2024-01-24 13:18:54,164] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:54,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:54,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:54,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:54,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000280765.1_ASM28076v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:54,191] [INFO] Task started: Blastn
[2024-01-24 13:18:54,191] [INFO] Running command: blastn -query GCF_000280765.1_ASM28076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg786fb02c-2dcb-4391-9d13-2499abe2b483/dqc_reference/reference_markers_gtdb.fasta -out GCF_000280765.1_ASM28076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:55,873] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:55,878] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:55,878] [INFO] Target genome list was writen to GCF_000280765.1_ASM28076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:55,895] [INFO] Task started: fastANI
[2024-01-24 13:18:55,896] [INFO] Running command: fastANI --query /var/lib/cwl/stga16f8fc9-de62-439f-bb73-3d7765e024fd/GCF_000280765.1_ASM28076v1_genomic.fna.gz --refList GCF_000280765.1_ASM28076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000280765.1_ASM28076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:20,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:20,645] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:20,646] [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_013386115.1	s__Pseudomonas_E gingeri_B	98.7691	2306	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	conclusive
GCF_013385635.1	s__Pseudomonas_E gingeri_A	93.8105	2208	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.63	99.24	0.97	0.93	14	-
GCF_900109755.1	s__Pseudomonas_E agarici	88.7292	1337	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.73	99.34	0.97	0.94	5	-
GCF_001293465.1	s__Pseudomonas_E fuscovaginae_B	87.7793	1715	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.24	0.95	0.95	2	-
GCF_000364705.1	s__Pseudomonas_E fuscovaginae_A	87.3944	1536	2524	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_014268755.2	s__Pseudomonas_E sp014268755	87.3773	1725	2524	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_000820515.1	s__Pseudomonas_E batumici	87.0256	1481	2524	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_900105475.1	s__Pseudomonas_E asplenii	86.9632	1604	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.96	97.58	0.90	0.87	7	-
GCF_013385425.1	s__Pseudomonas_E gingeri_D	86.9246	1685	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.70	0.93	0.93	2	-
GCF_002814235.1	s__Pseudomonas_E sp002814235	86.9066	1723	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.25	95.56	0.91	0.90	3	-
GCF_004011535.1	s__Pseudomonas_E asplenii_A	86.8498	1705	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	4	-
GCF_013386165.1	s__Pseudomonas_E gingeri_C	86.5915	1714	2524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.31	0.93	0.92	4	-
GCF_904067045.1	s__Pseudomonas_E sp904067045	86.3042	1499	2524	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 13:19:20,648] [INFO] GTDB search result was written to GCF_000280765.1_ASM28076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:20,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:20,656] [INFO] DFAST_QC result json was written to GCF_000280765.1_ASM28076v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:20,656] [INFO] DFAST_QC completed!
[2024-01-24 13:19:20,656] [INFO] Total running time: 0h2m15s