[2024-01-24 10:47:54,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,343] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg41118502-c3e3-4b4d-8bee-d7c3c389e427/GCF_020025155.1_ASM2002515v1_genomic.fna.gz | prodigal -d GCF_020025155.1_ASM2002515v1_genomic.fna/cds.fna -a GCF_020025155.1_ASM2002515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:15,376] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:15,376] [INFO] Task started: HMMsearch
[2024-01-24 10:48:15,376] [INFO] Running command: hmmsearch --tblout GCF_020025155.1_ASM2002515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference/reference_markers.hmm GCF_020025155.1_ASM2002515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:15,697] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:15,699] [INFO] Found 6/6 markers.
[2024-01-24 10:48:15,741] [INFO] Query marker FASTA was written to GCF_020025155.1_ASM2002515v1_genomic.fna/markers.fasta
[2024-01-24 10:48:15,742] [INFO] Task started: Blastn
[2024-01-24 10:48:15,742] [INFO] Running command: blastn -query GCF_020025155.1_ASM2002515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference/reference_markers.fasta -out GCF_020025155.1_ASM2002515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:16,713] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:16,719] [INFO] Selected 23 target genomes.
[2024-01-24 10:48:16,719] [INFO] Target genome list was writen to GCF_020025155.1_ASM2002515v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:16,739] [INFO] Task started: fastANI
[2024-01-24 10:48:16,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg41118502-c3e3-4b4d-8bee-d7c3c389e427/GCF_020025155.1_ASM2002515v1_genomic.fna.gz --refList GCF_020025155.1_ASM2002515v1_genomic.fna/target_genomes.txt --output GCF_020025155.1_ASM2002515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:33,569] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:33,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:33,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:33,592] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:33,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:33,592] [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
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.3632	415	1217	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.3225	424	1217	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	79.1013	428	1217	95	below_threshold
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	78.9988	374	1217	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.9501	403	1217	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.7526	459	1217	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.7218	456	1217	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	78.5685	372	1217	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.5475	338	1217	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	78.5333	368	1217	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.5277	442	1217	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.4865	321	1217	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	78.4356	346	1217	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	78.3748	340	1217	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.2716	310	1217	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	78.2707	313	1217	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	78.2042	297	1217	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	78.1642	329	1217	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	78.1507	310	1217	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	77.9614	316	1217	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	77.8858	337	1217	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	77.6535	212	1217	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	77.5645	206	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:33,594] [INFO] DFAST Taxonomy check result was written to GCF_020025155.1_ASM2002515v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:33,595] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:33,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:33,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference/checkm_data
[2024-01-24 10:48:33,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:33,646] [INFO] Task started: CheckM
[2024-01-24 10:48:33,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020025155.1_ASM2002515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020025155.1_ASM2002515v1_genomic.fna/checkm_input GCF_020025155.1_ASM2002515v1_genomic.fna/checkm_result
[2024-01-24 10:49:12,053] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:12,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:12,082] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:12,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:12,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020025155.1_ASM2002515v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:12,084] [INFO] Task started: Blastn
[2024-01-24 10:49:12,084] [INFO] Running command: blastn -query GCF_020025155.1_ASM2002515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc110d530-1155-4c00-b944-8d7617a60eaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_020025155.1_ASM2002515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:13,897] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:13,902] [INFO] Selected 15 target genomes.
[2024-01-24 10:49:13,902] [INFO] Target genome list was writen to GCF_020025155.1_ASM2002515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:13,963] [INFO] Task started: fastANI
[2024-01-24 10:49:13,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg41118502-c3e3-4b4d-8bee-d7c3c389e427/GCF_020025155.1_ASM2002515v1_genomic.fna.gz --refList GCF_020025155.1_ASM2002515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020025155.1_ASM2002515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:24,380] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:24,398] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:24,398] [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_900104945.1	s__Pseudomonas_D xinjiangensis	82.6407	867	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	79.3635	415	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	79.2101	463	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	79.1931	400	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	79.1851	467	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	79.1697	459	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008638305.1	s__Pseudomonas_D profundi	79.0985	427	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.49	98.49	0.91	0.91	2	-
GCF_003586265.1	s__Pseudomonas_D jilinensis	79.0091	470	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.07	95.47	0.89	0.88	3	-
GCF_900114825.1	s__Pseudomonas_D yangmingensis	78.9988	374	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.972	342	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	78.7453	419	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012735335.1	s__Pseudomonas_D sp012735335	78.5951	297	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	78.505	434	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	78.2593	341	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418465.1	s__Pseudomonas_O sp002418465	77.9329	300	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:24,400] [INFO] GTDB search result was written to GCF_020025155.1_ASM2002515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:24,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:24,406] [INFO] DFAST_QC result json was written to GCF_020025155.1_ASM2002515v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:24,407] [INFO] DFAST_QC completed!
[2024-01-24 10:49:24,407] [INFO] Total running time: 0h1m30s