[2024-01-24 14:20:01,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:01,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:01,244] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference
[2024-01-24 14:20:02,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,439] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,439] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd66c200-1723-4bde-8947-d1db9189c1b4/GCF_014358015.1_ASM1435801v1_genomic.fna.gz | prodigal -d GCF_014358015.1_ASM1435801v1_genomic.fna/cds.fna -a GCF_014358015.1_ASM1435801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:19,395] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:19,396] [INFO] Task started: HMMsearch
[2024-01-24 14:20:19,396] [INFO] Running command: hmmsearch --tblout GCF_014358015.1_ASM1435801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference/reference_markers.hmm GCF_014358015.1_ASM1435801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:19,694] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:19,695] [INFO] Found 6/6 markers.
[2024-01-24 14:20:19,737] [INFO] Query marker FASTA was written to GCF_014358015.1_ASM1435801v1_genomic.fna/markers.fasta
[2024-01-24 14:20:19,738] [INFO] Task started: Blastn
[2024-01-24 14:20:19,738] [INFO] Running command: blastn -query GCF_014358015.1_ASM1435801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference/reference_markers.fasta -out GCF_014358015.1_ASM1435801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:20,706] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:20,709] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:20,710] [INFO] Target genome list was writen to GCF_014358015.1_ASM1435801v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:20,727] [INFO] Task started: fastANI
[2024-01-24 14:20:20,728] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd66c200-1723-4bde-8947-d1db9189c1b4/GCF_014358015.1_ASM1435801v1_genomic.fna.gz --refList GCF_014358015.1_ASM1435801v1_genomic.fna/target_genomes.txt --output GCF_014358015.1_ASM1435801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:33,201] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:33,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:33,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:33,217] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:33,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:33,218] [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=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	87.6351	1374	1804	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	87.5797	1393	1804	95	below_threshold
Pseudomonas viridiflava	strain=ICMP2848	GCA_001401215.1	33069	33069	type	True	87.5439	1384	1804	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	87.5435	1414	1804	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	87.533	1467	1804	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	83.9597	1247	1804	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	83.4146	1259	1804	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	83.3827	1285	1804	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	80.2017	791	1804	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.7092	462	1804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:33,219] [INFO] DFAST Taxonomy check result was written to GCF_014358015.1_ASM1435801v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:33,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:33,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:33,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference/checkm_data
[2024-01-24 14:20:33,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:33,270] [INFO] Task started: CheckM
[2024-01-24 14:20:33,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014358015.1_ASM1435801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014358015.1_ASM1435801v1_genomic.fna/checkm_input GCF_014358015.1_ASM1435801v1_genomic.fna/checkm_result
[2024-01-24 14:21:25,496] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:25,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:25,520] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:25,520] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:25,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014358015.1_ASM1435801v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:25,521] [INFO] Task started: Blastn
[2024-01-24 14:21:25,521] [INFO] Running command: blastn -query GCF_014358015.1_ASM1435801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf43d17c-aed4-4bca-9096-dfc085758458/dqc_reference/reference_markers_gtdb.fasta -out GCF_014358015.1_ASM1435801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:27,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:27,358] [INFO] Selected 6 target genomes.
[2024-01-24 14:21:27,358] [INFO] Target genome list was writen to GCF_014358015.1_ASM1435801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:27,364] [INFO] Task started: fastANI
[2024-01-24 14:21:27,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd66c200-1723-4bde-8947-d1db9189c1b4/GCF_014358015.1_ASM1435801v1_genomic.fna.gz --refList GCF_014358015.1_ASM1435801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014358015.1_ASM1435801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:36,567] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:36,578] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:36,578] [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_014358015.1	s__Pseudomonas_E triticumensis	100.0	1803	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.53	98.52	0.94	0.92	3	conclusive
GCF_900143095.1	s__Pseudomonas_E asturiensis	94.7951	1659	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.96	0.95	0.95	2	-
GCF_002723575.1	s__Pseudomonas_E viridiflava_B	87.6398	1472	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.76	0.95	0.94	5	-
GCF_001642795.1	s__Pseudomonas_E viridiflava	87.533	1467	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	96.41	0.93	0.89	1379	-
GCF_003702045.1	s__Pseudomonas_E viridiflava_C	86.4751	1417	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.39	99.39	0.95	0.95	2	-
GCF_002087235.1	s__Pseudomonas_E floridensis	86.3094	1366	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:36,580] [INFO] GTDB search result was written to GCF_014358015.1_ASM1435801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:36,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:36,583] [INFO] DFAST_QC result json was written to GCF_014358015.1_ASM1435801v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:36,583] [INFO] DFAST_QC completed!
[2024-01-24 14:21:36,583] [INFO] Total running time: 0h1m35s