[2024-01-24 13:25:47,752] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,754] [INFO] DQC Reference Directory: /var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference
[2024-01-24 13:25:49,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,147] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg59e82425-b1bd-4fe6-932f-251d32cb556b/GCF_008801485.1_ASM880148v1_genomic.fna.gz | prodigal -d GCF_008801485.1_ASM880148v1_genomic.fna/cds.fna -a GCF_008801485.1_ASM880148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:06,135] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:06,136] [INFO] Task started: HMMsearch
[2024-01-24 13:26:06,136] [INFO] Running command: hmmsearch --tblout GCF_008801485.1_ASM880148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference/reference_markers.hmm GCF_008801485.1_ASM880148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:06,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:06,431] [INFO] Found 6/6 markers.
[2024-01-24 13:26:06,476] [INFO] Query marker FASTA was written to GCF_008801485.1_ASM880148v1_genomic.fna/markers.fasta
[2024-01-24 13:26:06,476] [INFO] Task started: Blastn
[2024-01-24 13:26:06,477] [INFO] Running command: blastn -query GCF_008801485.1_ASM880148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference/reference_markers.fasta -out GCF_008801485.1_ASM880148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:07,358] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:07,361] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:07,361] [INFO] Target genome list was writen to GCF_008801485.1_ASM880148v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:07,368] [INFO] Task started: fastANI
[2024-01-24 13:26:07,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e82425-b1bd-4fe6-932f-251d32cb556b/GCF_008801485.1_ASM880148v1_genomic.fna.gz --refList GCF_008801485.1_ASM880148v1_genomic.fna/target_genomes.txt --output GCF_008801485.1_ASM880148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:23,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:23,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:23,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:23,336] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:23,336] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:23,336] [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 psychrophila	strain=CCUG 53877	GCA_008801485.1	122355	122355	type	True	100.0	1739	1742	95	conclusive
Pseudomonas psychrophila	strain=DSM 17535	GCA_001043005.1	122355	122355	type	True	99.9955	1737	1742	95	conclusive
Pseudomonas deceptionensis	strain=DSM 26521	GCA_001042895.1	882211	882211	type	True	89.0982	1399	1742	95	below_threshold
Pseudomonas deceptionensis	strain=LMG 25555	GCA_900106095.1	882211	882211	type	True	89.059	1405	1742	95	below_threshold
Pseudomonas fragi	strain=NBRC 3458	GCA_002091615.1	296	296	type	True	87.5617	1317	1742	95	below_threshold
Pseudomonas fragi	strain=NRRL B-727	GCA_900105835.1	296	296	type	True	87.5549	1325	1742	95	below_threshold
Pseudomonas helleri	strain=DSM 29165	GCA_001043025.1	1608996	1608996	type	True	84.3799	1142	1742	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	81.4318	898	1742	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	81.2	903	1742	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	79.9572	633	1742	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	79.8861	612	1742	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	79.4133	740	1742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:23,338] [INFO] DFAST Taxonomy check result was written to GCF_008801485.1_ASM880148v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:23,339] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:23,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:23,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference/checkm_data
[2024-01-24 13:26:23,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:23,391] [INFO] Task started: CheckM
[2024-01-24 13:26:23,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801485.1_ASM880148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801485.1_ASM880148v1_genomic.fna/checkm_input GCF_008801485.1_ASM880148v1_genomic.fna/checkm_result
[2024-01-24 13:27:13,298] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:13,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:13,326] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:13,327] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:13,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801485.1_ASM880148v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:13,328] [INFO] Task started: Blastn
[2024-01-24 13:27:13,328] [INFO] Running command: blastn -query GCF_008801485.1_ASM880148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae0287ab-4e99-488e-9f42-cf3fa6b9abfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801485.1_ASM880148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:14,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:14,887] [INFO] Selected 9 target genomes.
[2024-01-24 13:27:14,888] [INFO] Target genome list was writen to GCF_008801485.1_ASM880148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:14,903] [INFO] Task started: fastANI
[2024-01-24 13:27:14,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg59e82425-b1bd-4fe6-932f-251d32cb556b/GCF_008801485.1_ASM880148v1_genomic.fna.gz --refList GCF_008801485.1_ASM880148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801485.1_ASM880148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:26,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:26,553] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:26,554] [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_001043005.1	s__Pseudomonas_E psychrophila	99.9955	1737	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.62	99.23	0.96	0.92	7	conclusive
GCF_900106095.1	s__Pseudomonas_E deceptionensis	89.059	1405	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002269505.1	s__Pseudomonas_E fragi_D	87.8209	1302	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.09	96.09	0.88	0.88	2	-
GCF_900105835.1	s__Pseudomonas_E fragi	87.5655	1323	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.76	96.96	0.94	0.89	28	-
GCF_900618535.1	s__Pseudomonas_E bubulae	87.441	1343	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.96	0.92	0.87	18	-
GCF_904063065.1	s__Pseudomonas_E paraversuta	85.6536	1211	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.22	0.95	0.95	9	-
GCF_001043025.1	s__Pseudomonas_E helleri	84.382	1141	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.29	96.40	0.86	0.80	22	-
GCF_001043055.1	s__Pseudomonas_E weihenstephanensis	84.3113	1039	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_001411475.1	s__Pseudomonas_E endophytica	82.9691	950	1742	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 13:27:26,556] [INFO] GTDB search result was written to GCF_008801485.1_ASM880148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:26,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:26,559] [INFO] DFAST_QC result json was written to GCF_008801485.1_ASM880148v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:26,560] [INFO] DFAST_QC completed!
[2024-01-24 13:27:26,560] [INFO] Total running time: 0h1m39s