[2024-01-24 11:12:57,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference
[2024-01-24 11:12:58,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:58,850] [INFO] Task started: Prodigal
[2024-01-24 11:12:58,851] [INFO] Running command: gunzip -c /var/lib/cwl/stga88eb3a4-3dd6-47ef-ba17-18d51302ae9e/GCF_002699855.1_ASM269985v1_genomic.fna.gz | prodigal -d GCF_002699855.1_ASM269985v1_genomic.fna/cds.fna -a GCF_002699855.1_ASM269985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:15,224] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:15,225] [INFO] Task started: HMMsearch
[2024-01-24 11:13:15,225] [INFO] Running command: hmmsearch --tblout GCF_002699855.1_ASM269985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference/reference_markers.hmm GCF_002699855.1_ASM269985v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:15,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:15,627] [INFO] Found 6/6 markers.
[2024-01-24 11:13:15,675] [INFO] Query marker FASTA was written to GCF_002699855.1_ASM269985v1_genomic.fna/markers.fasta
[2024-01-24 11:13:15,675] [INFO] Task started: Blastn
[2024-01-24 11:13:15,675] [INFO] Running command: blastn -query GCF_002699855.1_ASM269985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference/reference_markers.fasta -out GCF_002699855.1_ASM269985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:16,749] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:16,752] [INFO] Selected 13 target genomes.
[2024-01-24 11:13:16,752] [INFO] Target genome list was writen to GCF_002699855.1_ASM269985v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:16,757] [INFO] Task started: fastANI
[2024-01-24 11:13:16,758] [INFO] Running command: fastANI --query /var/lib/cwl/stga88eb3a4-3dd6-47ef-ba17-18d51302ae9e/GCF_002699855.1_ASM269985v1_genomic.fna.gz --refList GCF_002699855.1_ASM269985v1_genomic.fna/target_genomes.txt --output GCF_002699855.1_ASM269985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:36,593] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:36,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:36,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:36,605] [INFO] Found 13 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 11:13:36,605] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:13:36,605] [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 amygdali	strain=ICMP 3918	GCA_002699855.1	47877	47877	suspected-type	True	100.0	1731	1751	95	inconclusive
Pseudomonas amygdali	strain=CFBP 3205	GCA_000935645.1	47877	47877	suspected-type	True	99.9212	1678	1751	95	inconclusive
Pseudomonas savastanoi	strain=CFBP 5062	GCA_001538155.1	29438	29438	pathovar	True	98.8271	1627	1751	95	inconclusive
Pseudomonas savastanoi	strain=ICMP7711	GCA_001483545.1	29438	29438	pathovar	True	98.8245	1546	1751	95	inconclusive
Pseudomonas savastanoi	strain=ICMP4352	GCA_001401285.1	29438	29438	suspected-type	True	98.8055	1584	1751	95	inconclusive
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	98.7079	1616	1751	95	inconclusive
Pseudomonas meliae	strain=ICMP6289	GCA_001400515.1	86176	86176	suspected-type	True	98.4575	1342	1751	95	inconclusive
Pseudomonas meliae	strain=CFBP 3225	GCA_000935675.1	86176	86176	suspected-type	True	98.4372	1395	1751	95	inconclusive
Pseudomonas ficuserectae	strain=ICMP7848	GCA_001400815.1	53410	53410	type	True	97.5624	1361	1751	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	89.5357	1529	1751	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	89.4919	1536	1751	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	79.9253	668	1751	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	79.8681	704	1751	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:36,607] [INFO] DFAST Taxonomy check result was written to GCF_002699855.1_ASM269985v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:36,608] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:36,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:36,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference/checkm_data
[2024-01-24 11:13:36,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:36,665] [INFO] Task started: CheckM
[2024-01-24 11:13:36,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002699855.1_ASM269985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002699855.1_ASM269985v1_genomic.fna/checkm_input GCF_002699855.1_ASM269985v1_genomic.fna/checkm_result
[2024-01-24 11:14:27,368] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:27,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:27,386] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:27,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:27,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002699855.1_ASM269985v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:27,387] [INFO] Task started: Blastn
[2024-01-24 11:14:27,387] [INFO] Running command: blastn -query GCF_002699855.1_ASM269985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d1b49ae-f056-4f94-8c72-8fabef6a17fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_002699855.1_ASM269985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:29,245] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:29,249] [INFO] Selected 10 target genomes.
[2024-01-24 11:14:29,250] [INFO] Target genome list was writen to GCF_002699855.1_ASM269985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:29,257] [INFO] Task started: fastANI
[2024-01-24 11:14:29,258] [INFO] Running command: fastANI --query /var/lib/cwl/stga88eb3a4-3dd6-47ef-ba17-18d51302ae9e/GCF_002699855.1_ASM269985v1_genomic.fna.gz --refList GCF_002699855.1_ASM269985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002699855.1_ASM269985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:45,485] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:45,503] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:45,503] [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_002699855.1	s__Pseudomonas_E amygdali	100.0	1731	1751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	96.47	0.89	0.82	226	conclusive
GCF_900074915.1	s__Pseudomonas_E cerasi	89.9754	1546	1751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.51	98.33	0.88	0.83	51	-
GCF_001400735.1	s__Pseudomonas_E caricapapayae	89.5477	1517	1751	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_009176725.1	s__Pseudomonas_E syringae_M	89.5359	1498	1751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	98.71	98.38	0.92	0.88	59	-
GCF_900103225.1	s__Pseudomonas_E congelans	89.3757	1495	1751	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	89.3074	1518	1751	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_000444135.1	s__Pseudomonas_E avellanae	87.9731	1374	1751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	-
GCF_002093745.1	s__Pseudomonas_E graminis_C	86.4834	1437	1751	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_000452705.1	s__Pseudomonas_E syringae_F	86.2349	1408	1751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	86.212	1406	1751	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:45,505] [INFO] GTDB search result was written to GCF_002699855.1_ASM269985v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:45,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:45,511] [INFO] DFAST_QC result json was written to GCF_002699855.1_ASM269985v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:45,511] [INFO] DFAST_QC completed!
[2024-01-24 11:14:45,511] [INFO] Total running time: 0h1m48s