[2024-01-24 11:51:24,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,941] [INFO] DQC Reference Directory: /var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference
[2024-01-24 11:51:26,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,259] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,260] [INFO] Running command: gunzip -c /var/lib/cwl/stgc106a017-9309-47ce-8cd4-34b2b156c88f/GCF_002087235.1_ASM208723v1_genomic.fna.gz | prodigal -d GCF_002087235.1_ASM208723v1_genomic.fna/cds.fna -a GCF_002087235.1_ASM208723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:45,058] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:45,059] [INFO] Task started: HMMsearch
[2024-01-24 11:51:45,059] [INFO] Running command: hmmsearch --tblout GCF_002087235.1_ASM208723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference/reference_markers.hmm GCF_002087235.1_ASM208723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:45,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:45,403] [INFO] Found 6/6 markers.
[2024-01-24 11:51:45,456] [INFO] Query marker FASTA was written to GCF_002087235.1_ASM208723v1_genomic.fna/markers.fasta
[2024-01-24 11:51:45,456] [INFO] Task started: Blastn
[2024-01-24 11:51:45,457] [INFO] Running command: blastn -query GCF_002087235.1_ASM208723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference/reference_markers.fasta -out GCF_002087235.1_ASM208723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:46,363] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:46,367] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:46,368] [INFO] Target genome list was writen to GCF_002087235.1_ASM208723v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:46,371] [INFO] Task started: fastANI
[2024-01-24 11:51:46,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgc106a017-9309-47ce-8cd4-34b2b156c88f/GCF_002087235.1_ASM208723v1_genomic.fna.gz --refList GCF_002087235.1_ASM208723v1_genomic.fna/target_genomes.txt --output GCF_002087235.1_ASM208723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:00,368] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:00,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:00,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:00,379] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:00,380] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:00,380] [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 syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	86.9803	1409	1908	95	below_threshold
Pseudomonas viridiflava	strain=ICMP2848	GCA_001401215.1	33069	33069	type	True	86.9331	1438	1908	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	86.9202	1459	1908	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	86.9174	1439	1908	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	86.8755	1513	1908	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	83.9248	1306	1908	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	83.6856	1300	1908	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	83.512	1318	1908	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	83.3265	1333	1908	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	80.1829	731	1908	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	80.0502	770	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,383] [INFO] DFAST Taxonomy check result was written to GCF_002087235.1_ASM208723v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:00,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:00,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:00,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference/checkm_data
[2024-01-24 11:52:00,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:00,447] [INFO] Task started: CheckM
[2024-01-24 11:52:00,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002087235.1_ASM208723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002087235.1_ASM208723v1_genomic.fna/checkm_input GCF_002087235.1_ASM208723v1_genomic.fna/checkm_result
[2024-01-24 11:52:57,482] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:57,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:57,508] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:57,509] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:57,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002087235.1_ASM208723v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:57,510] [INFO] Task started: Blastn
[2024-01-24 11:52:57,510] [INFO] Running command: blastn -query GCF_002087235.1_ASM208723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb286d944-ca17-4427-b79a-7ee2d93293d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002087235.1_ASM208723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,961] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,965] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:58,965] [INFO] Target genome list was writen to GCF_002087235.1_ASM208723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:58,973] [INFO] Task started: fastANI
[2024-01-24 11:52:58,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgc106a017-9309-47ce-8cd4-34b2b156c88f/GCF_002087235.1_ASM208723v1_genomic.fna.gz --refList GCF_002087235.1_ASM208723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002087235.1_ASM208723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:13,763] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:13,782] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:13,783] [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_002087235.1	s__Pseudomonas_E floridensis	100.0	1900	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002723575.1	s__Pseudomonas_E viridiflava_B	87.1248	1518	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.76	0.95	0.94	5	-
GCF_001642795.1	s__Pseudomonas_E viridiflava	86.8755	1513	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	96.41	0.93	0.89	1379	-
GCF_003702045.1	s__Pseudomonas_E viridiflava_C	86.6669	1457	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.39	99.39	0.95	0.95	2	-
GCF_900143095.1	s__Pseudomonas_E asturiensis	86.3712	1456	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.96	0.95	0.95	2	-
GCF_014358015.1	s__Pseudomonas_E triticumensis	86.3706	1360	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.53	98.52	0.94	0.92	3	-
GCF_900103225.1	s__Pseudomonas_E congelans	84.0711	1325	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.60	98.04	0.95	0.92	20	-
GCF_000507185.2	s__Pseudomonas_E syringae	84.0338	1323	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	97.83	96.00	0.92	0.85	147	-
GCF_001400735.1	s__Pseudomonas_E caricapapayae	83.5657	1314	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	97.41	0.91	0.88	11	-
GCF_001401155.1	s__Pseudomonas_E tremae	83.2977	1235	1908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.42	0.92	0.88	76	-
GCF_003700275.1	s__Pseudomonas_E cichorii_B	83.2205	1138	1908	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 11:53:13,786] [INFO] GTDB search result was written to GCF_002087235.1_ASM208723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:13,786] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:13,791] [INFO] DFAST_QC result json was written to GCF_002087235.1_ASM208723v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:13,791] [INFO] DFAST_QC completed!
[2024-01-24 11:53:13,791] [INFO] Total running time: 0h1m49s