[2024-01-24 12:47:22,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,375] [INFO] DQC Reference Directory: /var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference
[2024-01-24 12:47:23,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,613] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d5400ff-5062-4a9b-a9bc-537f1a5acf8a/GCF_002307495.1_ASM230749v1_genomic.fna.gz | prodigal -d GCF_002307495.1_ASM230749v1_genomic.fna/cds.fna -a GCF_002307495.1_ASM230749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:36,433] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:36,433] [INFO] Task started: HMMsearch
[2024-01-24 12:47:36,433] [INFO] Running command: hmmsearch --tblout GCF_002307495.1_ASM230749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference/reference_markers.hmm GCF_002307495.1_ASM230749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:36,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:36,722] [INFO] Found 6/6 markers.
[2024-01-24 12:47:36,767] [INFO] Query marker FASTA was written to GCF_002307495.1_ASM230749v1_genomic.fna/markers.fasta
[2024-01-24 12:47:36,767] [INFO] Task started: Blastn
[2024-01-24 12:47:36,767] [INFO] Running command: blastn -query GCF_002307495.1_ASM230749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference/reference_markers.fasta -out GCF_002307495.1_ASM230749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:37,835] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:37,839] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:37,839] [INFO] Target genome list was writen to GCF_002307495.1_ASM230749v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:37,845] [INFO] Task started: fastANI
[2024-01-24 12:47:37,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d5400ff-5062-4a9b-a9bc-537f1a5acf8a/GCF_002307495.1_ASM230749v1_genomic.fna.gz --refList GCF_002307495.1_ASM230749v1_genomic.fna/target_genomes.txt --output GCF_002307495.1_ASM230749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:47,411] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:47,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:47,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:47,422] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:47,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:47,423] [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 pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	90.3133	1075	1406	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	90.2746	1105	1406	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	84.9537	953	1406	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	84.8924	940	1406	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	84.7947	871	1406	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	84.7749	882	1406	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.5146	369	1406	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	78.4971	375	1406	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	78.4328	409	1406	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	78.4263	370	1406	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.372	427	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:47,426] [INFO] DFAST Taxonomy check result was written to GCF_002307495.1_ASM230749v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:47,426] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:47,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:47,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference/checkm_data
[2024-01-24 12:47:47,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:47,473] [INFO] Task started: CheckM
[2024-01-24 12:47:47,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002307495.1_ASM230749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002307495.1_ASM230749v1_genomic.fna/checkm_input GCF_002307495.1_ASM230749v1_genomic.fna/checkm_result
[2024-01-24 12:48:28,909] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:28,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:28,934] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:28,935] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:28,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002307495.1_ASM230749v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:28,935] [INFO] Task started: Blastn
[2024-01-24 12:48:28,935] [INFO] Running command: blastn -query GCF_002307495.1_ASM230749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga964e539-c32f-4980-b31d-9e2b3e854c03/dqc_reference/reference_markers_gtdb.fasta -out GCF_002307495.1_ASM230749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:30,726] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:30,729] [INFO] Selected 7 target genomes.
[2024-01-24 12:48:30,729] [INFO] Target genome list was writen to GCF_002307495.1_ASM230749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:30,751] [INFO] Task started: fastANI
[2024-01-24 12:48:30,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d5400ff-5062-4a9b-a9bc-537f1a5acf8a/GCF_002307495.1_ASM230749v1_genomic.fna.gz --refList GCF_002307495.1_ASM230749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002307495.1_ASM230749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:37,354] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:37,361] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:37,361] [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_003444685.1	s__Pseudomonas_D gallaeciensis	97.833	1184	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	conclusive
GCF_900114765.1	s__Pseudomonas_D pachastrellae	90.2889	1104	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	86.4647	859	1406	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_002903165.1	s__Pseudomonas_D oceani	84.9116	940	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	84.7909	881	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	81.6725	781	1406	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_008365385.1	s__Pseudomonas_D laoshanensis	78.6652	477	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:37,363] [INFO] GTDB search result was written to GCF_002307495.1_ASM230749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:37,363] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:37,366] [INFO] DFAST_QC result json was written to GCF_002307495.1_ASM230749v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:37,366] [INFO] DFAST_QC completed!
[2024-01-24 12:48:37,366] [INFO] Total running time: 0h1m15s