[2024-01-24 13:21:47,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,119] [INFO] DQC Reference Directory: /var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference
[2024-01-24 13:21:48,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,477] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dae7ac4-46a4-48ce-a448-69056bae479d/GCF_002091595.1_ASM209159v1_genomic.fna.gz | prodigal -d GCF_002091595.1_ASM209159v1_genomic.fna/cds.fna -a GCF_002091595.1_ASM209159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:09,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:09,929] [INFO] Task started: HMMsearch
[2024-01-24 13:22:09,929] [INFO] Running command: hmmsearch --tblout GCF_002091595.1_ASM209159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference/reference_markers.hmm GCF_002091595.1_ASM209159v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:10,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:10,415] [INFO] Found 6/6 markers.
[2024-01-24 13:22:10,476] [INFO] Query marker FASTA was written to GCF_002091595.1_ASM209159v1_genomic.fna/markers.fasta
[2024-01-24 13:22:10,476] [INFO] Task started: Blastn
[2024-01-24 13:22:10,476] [INFO] Running command: blastn -query GCF_002091595.1_ASM209159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference/reference_markers.fasta -out GCF_002091595.1_ASM209159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:11,450] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:11,453] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:11,454] [INFO] Target genome list was writen to GCF_002091595.1_ASM209159v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:11,462] [INFO] Task started: fastANI
[2024-01-24 13:22:11,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dae7ac4-46a4-48ce-a448-69056bae479d/GCF_002091595.1_ASM209159v1_genomic.fna.gz --refList GCF_002091595.1_ASM209159v1_genomic.fna/target_genomes.txt --output GCF_002091595.1_ASM209159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:32,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:32,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:32,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:32,859] [INFO] Found 14 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:22:32,859] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:32,859] [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 fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	100.0	2080	2086	95	conclusive
Pseudomonas fluorescens	strain=ATCC 13525	GCA_900215245.1	294	294	suspected-type	True	99.9966	2086	2086	95	conclusive
Pseudomonas fluorescens	strain=DSM 50090	GCA_001269845.1	294	294	suspected-type	True	99.9962	2062	2086	95	conclusive
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	99.9953	2060	2086	95	conclusive
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	99.9929	2086	2086	95	conclusive
Pseudomonas fluorescens	strain=ATCC 13525	GCA_002943685.1	294	294	suspected-type	True	99.9724	2046	2086	95	conclusive
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.2223	1576	2086	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.0076	1611	2086	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.9454	1603	2086	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.9291	1486	2086	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.1426	1310	2086	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	81.2918	912	2086	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.6094	573	2086	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	78.2069	497	2086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:32,860] [INFO] DFAST Taxonomy check result was written to GCF_002091595.1_ASM209159v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:32,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:32,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:32,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference/checkm_data
[2024-01-24 13:22:32,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:32,925] [INFO] Task started: CheckM
[2024-01-24 13:22:32,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091595.1_ASM209159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091595.1_ASM209159v1_genomic.fna/checkm_input GCF_002091595.1_ASM209159v1_genomic.fna/checkm_result
[2024-01-24 13:23:35,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:35,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:35,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:35,960] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:35,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091595.1_ASM209159v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:35,961] [INFO] Task started: Blastn
[2024-01-24 13:23:35,961] [INFO] Running command: blastn -query GCF_002091595.1_ASM209159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1884e96-185a-4b62-b7b1-0d77145c563f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091595.1_ASM209159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:37,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:37,393] [INFO] Selected 19 target genomes.
[2024-01-24 13:23:37,394] [INFO] Target genome list was writen to GCF_002091595.1_ASM209159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:37,411] [INFO] Task started: fastANI
[2024-01-24 13:23:37,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dae7ac4-46a4-48ce-a448-69056bae479d/GCF_002091595.1_ASM209159v1_genomic.fna.gz --refList GCF_002091595.1_ASM209159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091595.1_ASM209159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:07,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:07,151] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:07,151] [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_900215245.1	s__Pseudomonas_E fluorescens	99.9966	2086	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	conclusive
GCF_001647715.1	s__Pseudomonas_E antarctica_A	94.7103	1835	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_009707325.1	s__Pseudomonas_E sp002263605	90.0612	1644	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.58	0.94	0.94	2	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	89.7347	1762	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
GCF_900624995.1	s__Pseudomonas_E antarctica	89.57	1589	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	1.00	1.00	3	-
GCF_005938045.2	s__Pseudomonas_E sp005938045	89.5104	1721	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.18	95.16	0.86	0.86	3	-
GCF_013385965.1	s__Pseudomonas_E edaphica	89.5085	1741	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_900107155.1	s__Pseudomonas_E salomonii	89.4884	1731	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	89.4609	1709	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_002251635.1	s__Pseudomonas_E mandelii_B	88.8809	1259	2086	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_900580675.1	s__Pseudomonas_E sp900580675	88.6002	1487	2086	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_900591205.1	s__Pseudomonas_E sp900591205	88.4294	1619	2086	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_002843605.1	s__Pseudomonas_E sp002843605	88.2885	1606	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_900105325.1	s__Pseudomonas_E marginalis	88.219	1610	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_001439695.1	s__Pseudomonas_E veronii	88.0394	1542	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_009296165.1	s__Pseudomonas_E kitaguniensis	87.8931	1401	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.01	96.76	0.90	0.88	5	-
GCF_001439845.1	s__Pseudomonas_E lactis	87.4656	1555	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_900105675.1	s__Pseudomonas_E synxantha	87.3963	1568	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_001439815.1	s__Pseudomonas_E orientalis	87.2437	1524	2086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.01	96.05	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:07,153] [INFO] GTDB search result was written to GCF_002091595.1_ASM209159v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:07,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:07,160] [INFO] DFAST_QC result json was written to GCF_002091595.1_ASM209159v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:07,160] [INFO] DFAST_QC completed!
[2024-01-24 13:24:07,160] [INFO] Total running time: 0h2m20s