[2024-01-24 15:26:54,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference
[2024-01-24 15:26:55,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:55,874] [INFO] Task started: Prodigal
[2024-01-24 15:26:55,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ed82b38-fd55-46d3-a056-d9b36d82a903/GCF_008692855.1_ASM869285v1_genomic.fna.gz | prodigal -d GCF_008692855.1_ASM869285v1_genomic.fna/cds.fna -a GCF_008692855.1_ASM869285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:17,184] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:17,185] [INFO] Task started: HMMsearch
[2024-01-24 15:27:17,185] [INFO] Running command: hmmsearch --tblout GCF_008692855.1_ASM869285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference/reference_markers.hmm GCF_008692855.1_ASM869285v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:17,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:17,561] [INFO] Found 6/6 markers.
[2024-01-24 15:27:17,682] [INFO] Query marker FASTA was written to GCF_008692855.1_ASM869285v1_genomic.fna/markers.fasta
[2024-01-24 15:27:17,683] [INFO] Task started: Blastn
[2024-01-24 15:27:17,683] [INFO] Running command: blastn -query GCF_008692855.1_ASM869285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference/reference_markers.fasta -out GCF_008692855.1_ASM869285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:18,693] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:18,697] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:18,697] [INFO] Target genome list was writen to GCF_008692855.1_ASM869285v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:18,703] [INFO] Task started: fastANI
[2024-01-24 15:27:18,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed82b38-fd55-46d3-a056-d9b36d82a903/GCF_008692855.1_ASM869285v1_genomic.fna.gz --refList GCF_008692855.1_ASM869285v1_genomic.fna/target_genomes.txt --output GCF_008692855.1_ASM869285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:36,234] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:36,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:36,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:36,246] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {317: 'Pseudomonas syringae', 251699: 'Pseudomonas syringae group genomosp. 7', 251701: 'Pseudomonas syringae group genomosp. 3'}, {}
[2024-01-24 15:27:36,246] [INFO] Found 12 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 15:27:36,246] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:27:36,246] [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 caricapapayae	strain=CCUG 32775T	GCA_008692855.1	46678	46678	type	True	100.0	2060	2062	95	inconclusive
Pseudomonas caricapapayae	strain=ICMP2855	GCA_001400735.1	46678	46678	type	True	99.9469	1946	2062	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	97.6193	1804	2062	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_001401315.1	251699	251699	pathovar	True	97.5586	1753	2062	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	97.46	1825	2062	95	inconclusive
Pseudomonas syringae group genomosp. 7	strain=ICMP 4531	GCA_001400835.1	251699	251699	type	True	97.4103	1730	2062	95	inconclusive
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	89.4399	1671	2062	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	86.9856	1570	2062	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	79.6395	699	2062	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	79.54	724	2062	95	below_threshold
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	76.8456	233	2062	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	75.7866	60	2062	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,249] [INFO] DFAST Taxonomy check result was written to GCF_008692855.1_ASM869285v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:36,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:36,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:36,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference/checkm_data
[2024-01-24 15:27:36,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:36,308] [INFO] Task started: CheckM
[2024-01-24 15:27:36,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008692855.1_ASM869285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008692855.1_ASM869285v1_genomic.fna/checkm_input GCF_008692855.1_ASM869285v1_genomic.fna/checkm_result
[2024-01-24 15:28:39,425] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:39,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:39,446] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:39,446] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:39,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008692855.1_ASM869285v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:39,447] [INFO] Task started: Blastn
[2024-01-24 15:28:39,447] [INFO] Running command: blastn -query GCF_008692855.1_ASM869285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ed61b2f-e20a-4526-8dcd-0ff79c638510/dqc_reference/reference_markers_gtdb.fasta -out GCF_008692855.1_ASM869285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:40,959] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:40,962] [INFO] Selected 16 target genomes.
[2024-01-24 15:28:40,962] [INFO] Target genome list was writen to GCF_008692855.1_ASM869285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:40,973] [INFO] Task started: fastANI
[2024-01-24 15:28:40,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed82b38-fd55-46d3-a056-d9b36d82a903/GCF_008692855.1_ASM869285v1_genomic.fna.gz --refList GCF_008692855.1_ASM869285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008692855.1_ASM869285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:01,496] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:01,507] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:01,507] [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_001400735.1	s__Pseudomonas_E caricapapayae	99.9469	1946	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	97.41	0.91	0.88	11	conclusive
GCF_002699855.1	s__Pseudomonas_E amygdali	89.506	1550	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	96.47	0.89	0.82	226	-
GCF_009176725.1	s__Pseudomonas_E syringae_M	88.5818	1600	2062	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	88.5433	1635	2062	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_900074915.1	s__Pseudomonas_E cerasi	88.4486	1655	2062	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_000507185.2	s__Pseudomonas_E syringae	88.3482	1663	2062	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	86.9112	1446	2062	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	86.0539	1511	2062	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_900100365.1	s__Pseudomonas_E cannabina	85.599	1524	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.50	95.44	0.90	0.84	17	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	85.5264	1506	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
GCF_001401155.1	s__Pseudomonas_E tremae	85.3948	1497	2062	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_002087235.1	s__Pseudomonas_E floridensis	83.4451	1370	2062	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_002304225.1	s__Pseudomonas_E sp002304225	78.7681	422	2062	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:01,509] [INFO] GTDB search result was written to GCF_008692855.1_ASM869285v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:01,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:01,512] [INFO] DFAST_QC result json was written to GCF_008692855.1_ASM869285v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:01,513] [INFO] DFAST_QC completed!
[2024-01-24 15:29:01,513] [INFO] Total running time: 0h2m7s