[2024-01-24 14:30:34,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference
[2024-01-24 14:30:35,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,668] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d34a336-1e7c-47d9-8354-4ac0181f0d32/GCF_014646575.1_ASM1464657v1_genomic.fna.gz | prodigal -d GCF_014646575.1_ASM1464657v1_genomic.fna/cds.fna -a GCF_014646575.1_ASM1464657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:45,423] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:45,423] [INFO] Task started: HMMsearch
[2024-01-24 14:30:45,423] [INFO] Running command: hmmsearch --tblout GCF_014646575.1_ASM1464657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference/reference_markers.hmm GCF_014646575.1_ASM1464657v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:45,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:45,729] [INFO] Found 6/6 markers.
[2024-01-24 14:30:45,761] [INFO] Query marker FASTA was written to GCF_014646575.1_ASM1464657v1_genomic.fna/markers.fasta
[2024-01-24 14:30:45,761] [INFO] Task started: Blastn
[2024-01-24 14:30:45,762] [INFO] Running command: blastn -query GCF_014646575.1_ASM1464657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference/reference_markers.fasta -out GCF_014646575.1_ASM1464657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:46,825] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:46,829] [INFO] Selected 19 target genomes.
[2024-01-24 14:30:46,830] [INFO] Target genome list was writen to GCF_014646575.1_ASM1464657v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:46,836] [INFO] Task started: fastANI
[2024-01-24 14:30:46,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d34a336-1e7c-47d9-8354-4ac0181f0d32/GCF_014646575.1_ASM1464657v1_genomic.fna.gz --refList GCF_014646575.1_ASM1464657v1_genomic.fna/target_genomes.txt --output GCF_014646575.1_ASM1464657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:02,084] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:02,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:02,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:02,102] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:02,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:02,103] [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
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	81.4285	662	1013	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	81.3969	669	1013	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	80.7155	638	1013	95	below_threshold
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	79.3275	414	1013	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	79.283	454	1013	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.2269	448	1013	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	79.1628	411	1013	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	79.0046	426	1013	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	78.9589	405	1013	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.8749	362	1013	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	78.8736	411	1013	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	78.8577	383	1013	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	78.7154	433	1013	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.715	429	1013	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	78.6009	345	1013	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.5532	385	1013	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	78.4623	373	1013	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	78.3647	377	1013	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.3255	391	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:02,107] [INFO] DFAST Taxonomy check result was written to GCF_014646575.1_ASM1464657v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:02,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:02,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:02,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference/checkm_data
[2024-01-24 14:31:02,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:02,147] [INFO] Task started: CheckM
[2024-01-24 14:31:02,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646575.1_ASM1464657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646575.1_ASM1464657v1_genomic.fna/checkm_input GCF_014646575.1_ASM1464657v1_genomic.fna/checkm_result
[2024-01-24 14:31:36,695] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:36,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:36,714] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:36,714] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:36,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646575.1_ASM1464657v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:36,715] [INFO] Task started: Blastn
[2024-01-24 14:31:36,716] [INFO] Running command: blastn -query GCF_014646575.1_ASM1464657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg538b76bc-5737-4106-ba69-73be41b69d2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646575.1_ASM1464657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:38,549] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:38,554] [INFO] Selected 8 target genomes.
[2024-01-24 14:31:38,555] [INFO] Target genome list was writen to GCF_014646575.1_ASM1464657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:38,561] [INFO] Task started: fastANI
[2024-01-24 14:31:38,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d34a336-1e7c-47d9-8354-4ac0181f0d32/GCF_014646575.1_ASM1464657v1_genomic.fna.gz --refList GCF_014646575.1_ASM1464657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646575.1_ASM1464657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:45,838] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:45,847] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:45,848] [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_014646575.1	s__Pseudomonas_D pertucinogena	100.0	1012	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115905.1	s__Pseudomonas_D formosensis	83.7333	770	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCA_012735335.1	s__Pseudomonas_D sp012735335	83.4635	539	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	82.9594	741	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	82.4822	740	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	82.2592	733	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	81.8125	558	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	81.4098	667	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:45,850] [INFO] GTDB search result was written to GCF_014646575.1_ASM1464657v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:45,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:45,854] [INFO] DFAST_QC result json was written to GCF_014646575.1_ASM1464657v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:45,854] [INFO] DFAST_QC completed!
[2024-01-24 14:31:45,854] [INFO] Total running time: 0h1m11s