[2024-01-25 19:04:35,648] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:35,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:35,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference
[2024-01-25 19:04:36,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:36,812] [INFO] Task started: Prodigal
[2024-01-25 19:04:36,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg38358f90-c6b6-4a81-88a2-6fce39f65b2b/GCF_028993425.1_ASM2899342v1_genomic.fna.gz | prodigal -d GCF_028993425.1_ASM2899342v1_genomic.fna/cds.fna -a GCF_028993425.1_ASM2899342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:58,653] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:58,653] [INFO] Task started: HMMsearch
[2024-01-25 19:04:58,653] [INFO] Running command: hmmsearch --tblout GCF_028993425.1_ASM2899342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference/reference_markers.hmm GCF_028993425.1_ASM2899342v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:58,927] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:58,928] [INFO] Found 6/6 markers.
[2024-01-25 19:04:58,976] [INFO] Query marker FASTA was written to GCF_028993425.1_ASM2899342v1_genomic.fna/markers.fasta
[2024-01-25 19:04:58,977] [INFO] Task started: Blastn
[2024-01-25 19:04:58,977] [INFO] Running command: blastn -query GCF_028993425.1_ASM2899342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference/reference_markers.fasta -out GCF_028993425.1_ASM2899342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:59,888] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:59,891] [INFO] Selected 16 target genomes.
[2024-01-25 19:04:59,891] [INFO] Target genome list was writen to GCF_028993425.1_ASM2899342v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:59,898] [INFO] Task started: fastANI
[2024-01-25 19:04:59,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg38358f90-c6b6-4a81-88a2-6fce39f65b2b/GCF_028993425.1_ASM2899342v1_genomic.fna.gz --refList GCF_028993425.1_ASM2899342v1_genomic.fna/target_genomes.txt --output GCF_028993425.1_ASM2899342v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:24,757] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:24,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:24,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:24,767] [WARNING] Following organisms are indistinguishable with ANI. [Pseudomonas syringae(317), Pseudomonas syringae group genomosp. 7(251699), Pseudomonas syringae group genomosp. 3(251701)]
[2024-01-25 19:05:24,767] [INFO] Found 16 fastANI hits (11 hits with ANI > threshold)
[2024-01-25 19:05:24,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:24,768] [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=DC3000	GCA_000007805.1	251701	251701	type	True	99.9912	2044	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP 2844	GCA_001401135.1	251701	251701	pathovar	True	99.8881	1897	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=CFBP 1657	GCA_000935725.1	251701	251701	pathovar	True	98.9824	1784	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP 3935	GCA_001400855.1	251701	251701	pathovar	True	98.867	1770	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP4303	GCA_001401395.1	251701	251701	pathovar	True	98.761	1696	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	98.6938	1705	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	98.6635	1738	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP2814	GCA_001401385.1	251701	251701	pathovar	True	98.6573	1728	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=CFBP 1702	GCA_000935765.1	251701	251701	pathovar	True	96.103	1716	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	96.0369	1642	2048	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	95.914	1586	2048	95	conclusive
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	87.7584	1539	2048	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	86.8529	1595	2048	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	86.7408	1589	2048	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	79.533	697	2048	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	79.4706	711	2048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:24,769] [INFO] DFAST Taxonomy check result was written to GCF_028993425.1_ASM2899342v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:24,769] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:24,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:24,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference/checkm_data
[2024-01-25 19:05:24,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:24,833] [INFO] Task started: CheckM
[2024-01-25 19:05:24,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028993425.1_ASM2899342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028993425.1_ASM2899342v1_genomic.fna/checkm_input GCF_028993425.1_ASM2899342v1_genomic.fna/checkm_result
[2024-01-25 19:06:29,298] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:29,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:29,320] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:29,320] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:29,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028993425.1_ASM2899342v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:29,321] [INFO] Task started: Blastn
[2024-01-25 19:06:29,321] [INFO] Running command: blastn -query GCF_028993425.1_ASM2899342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f67565-dd93-4478-bdbe-ebc515dd7c30/dqc_reference/reference_markers_gtdb.fasta -out GCF_028993425.1_ASM2899342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:31,088] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:31,092] [INFO] Selected 11 target genomes.
[2024-01-25 19:06:31,092] [INFO] Target genome list was writen to GCF_028993425.1_ASM2899342v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:31,121] [INFO] Task started: fastANI
[2024-01-25 19:06:31,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg38358f90-c6b6-4a81-88a2-6fce39f65b2b/GCF_028993425.1_ASM2899342v1_genomic.fna.gz --refList GCF_028993425.1_ASM2899342v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028993425.1_ASM2899342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:48,805] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:48,813] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:48,813] [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_000444135.1	s__Pseudomonas_E avellanae	95.4216	1518	2048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	conclusive
GCF_002699855.1	s__Pseudomonas_E amygdali	87.7524	1455	2048	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_900100365.1	s__Pseudomonas_E cannabina	87.7322	1548	2048	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	87.6925	1530	2048	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_002093745.1	s__Pseudomonas_E graminis_C	87.4257	1498	2048	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_009176725.1	s__Pseudomonas_E syringae_M	87.1894	1559	2048	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_900074915.1	s__Pseudomonas_E cerasi	87.105	1555	2048	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_001466965.1	s__Pseudomonas_E syringae_Q	87.0119	1472	2048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.87	0.94	0.94	3	-
GCF_000507185.2	s__Pseudomonas_E syringae	86.9627	1539	2048	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_900103225.1	s__Pseudomonas_E congelans	86.9069	1505	2048	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_000452705.1	s__Pseudomonas_E syringae_F	86.6701	1483	2048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:48,814] [INFO] GTDB search result was written to GCF_028993425.1_ASM2899342v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:48,815] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:48,819] [INFO] DFAST_QC result json was written to GCF_028993425.1_ASM2899342v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:48,819] [INFO] DFAST_QC completed!
[2024-01-25 19:06:48,819] [INFO] Total running time: 0h2m13s