[2024-01-24 13:48:59,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference
[2024-01-24 13:49:01,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,161] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg74a9cef2-61e2-459b-803c-bdbf62383466/GCF_002091795.1_ASM209179v1_genomic.fna.gz | prodigal -d GCF_002091795.1_ASM209179v1_genomic.fna/cds.fna -a GCF_002091795.1_ASM209179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,917] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,918] [INFO] Running command: hmmsearch --tblout GCF_002091795.1_ASM209179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference/reference_markers.hmm GCF_002091795.1_ASM209179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:24,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:24,278] [INFO] Found 6/6 markers.
[2024-01-24 13:49:24,333] [INFO] Query marker FASTA was written to GCF_002091795.1_ASM209179v1_genomic.fna/markers.fasta
[2024-01-24 13:49:24,334] [INFO] Task started: Blastn
[2024-01-24 13:49:24,334] [INFO] Running command: blastn -query GCF_002091795.1_ASM209179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference/reference_markers.fasta -out GCF_002091795.1_ASM209179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:25,217] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:25,220] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:25,221] [INFO] Target genome list was writen to GCF_002091795.1_ASM209179v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:25,226] [INFO] Task started: fastANI
[2024-01-24 13:49:25,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a9cef2-61e2-459b-803c-bdbf62383466/GCF_002091795.1_ASM209179v1_genomic.fna.gz --refList GCF_002091795.1_ASM209179v1_genomic.fna/target_genomes.txt --output GCF_002091795.1_ASM209179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:53,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:53,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:53,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:53,120] [INFO] Found 14 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:49:53,120] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:49:53,120] [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 synxantha	strain=NBRC 3913	GCA_002091795.1	47883	47883	type	True	100.0	2215	2220	95	inconclusive
Pseudomonas synxantha	strain=NCTC10696	GCA_901482615.1	47883	47883	type	True	99.9982	2219	2220	95	inconclusive
Pseudomonas synxantha	strain=LMG 2190	GCA_900105675.1	47883	47883	type	True	99.9982	2219	2220	95	inconclusive
Pseudomonas synxantha	strain=DSM 18928	GCA_001439725.1	47883	47883	type	True	99.9954	2207	2220	95	inconclusive
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	95.6881	1802	2220	95	inconclusive
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	89.7768	1615	2220	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	87.9186	1605	2220	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.6921	1574	2220	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.4939	1548	2220	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.6289	1456	2220	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	84.9873	1278	2220	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	81.4199	956	2220	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.9147	560	2220	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	78.4354	525	2220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:53,123] [INFO] DFAST Taxonomy check result was written to GCF_002091795.1_ASM209179v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:53,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:53,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:53,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference/checkm_data
[2024-01-24 13:49:53,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:53,198] [INFO] Task started: CheckM
[2024-01-24 13:49:53,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091795.1_ASM209179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091795.1_ASM209179v1_genomic.fna/checkm_input GCF_002091795.1_ASM209179v1_genomic.fna/checkm_result
[2024-01-24 13:50:59,510] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:59,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:59,540] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:59,540] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:59,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091795.1_ASM209179v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:59,541] [INFO] Task started: Blastn
[2024-01-24 13:50:59,542] [INFO] Running command: blastn -query GCF_002091795.1_ASM209179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a5784ac-a008-420f-86c5-3bddfb24f296/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091795.1_ASM209179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:00,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:00,893] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:00,893] [INFO] Target genome list was writen to GCF_002091795.1_ASM209179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:00,911] [INFO] Task started: fastANI
[2024-01-24 13:51:00,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg74a9cef2-61e2-459b-803c-bdbf62383466/GCF_002091795.1_ASM209179v1_genomic.fna.gz --refList GCF_002091795.1_ASM209179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091795.1_ASM209179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:27,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:27,406] [INFO] Found 15 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:51:27,407] [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_900105675.1	s__Pseudomonas_E synxantha	99.9982	2219	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	inconclusive
GCF_001439685.1	s__Pseudomonas_E libanensis	95.6822	1802	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	97.93	95.87	0.95	0.89	3	-
GCF_003851495.1	s__Pseudomonas_E fluorescens_BB	95.4428	1831	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3929	98.85	97.70	0.94	0.89	3	inconclusive
GCF_009659625.1	s__Pseudomonas_E haemolytica	91.2437	1662	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	90.4202	1699	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_001439845.1	s__Pseudomonas_E lactis	89.8431	1710	2220	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_001439735.1	s__Pseudomonas_E paralactis	89.8026	1611	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	-
GCF_003851685.1	s__Pseudomonas_E sp003851685	88.1861	1610	2220	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_003097075.1	s__Pseudomonas_E sp003097075	88.0728	1512	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_001439695.1	s__Pseudomonas_E veronii	87.9536	1558	2220	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_014207255.1	s__Pseudomonas_E sp014207255	87.91	1587	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.31	98.90	0.95	0.91	5	-
GCF_900107155.1	s__Pseudomonas_E salomonii	87.708	1608	2220	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_019139815.1	s__Pseudomonas_E sp900005815	87.4425	1504	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_007858255.1	s__Pseudomonas_E rhodesiae	86.7294	1498	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.21	97.47	0.91	0.84	28	-
GCF_017980685.1	s__Pseudomonas_E iridis	82.7834	1150	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:27,409] [INFO] GTDB search result was written to GCF_002091795.1_ASM209179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:27,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:27,414] [INFO] DFAST_QC result json was written to GCF_002091795.1_ASM209179v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:27,414] [INFO] DFAST_QC completed!
[2024-01-24 13:51:27,414] [INFO] Total running time: 0h2m28s