[2024-01-24 12:22:28,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,547] [INFO] DQC Reference Directory: /var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference
[2024-01-24 12:22:29,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,958] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,958] [INFO] Running command: gunzip -c /var/lib/cwl/stge7391ed8-0b8a-4e0e-a8ed-b358d0124744/GCF_000382145.1_ASM38214v1_genomic.fna.gz | prodigal -d GCF_000382145.1_ASM38214v1_genomic.fna/cds.fna -a GCF_000382145.1_ASM38214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:37,003] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:37,003] [INFO] Task started: HMMsearch
[2024-01-24 12:22:37,003] [INFO] Running command: hmmsearch --tblout GCF_000382145.1_ASM38214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference/reference_markers.hmm GCF_000382145.1_ASM38214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:37,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:37,304] [INFO] Found 6/6 markers.
[2024-01-24 12:22:37,335] [INFO] Query marker FASTA was written to GCF_000382145.1_ASM38214v1_genomic.fna/markers.fasta
[2024-01-24 12:22:37,336] [INFO] Task started: Blastn
[2024-01-24 12:22:37,336] [INFO] Running command: blastn -query GCF_000382145.1_ASM38214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference/reference_markers.fasta -out GCF_000382145.1_ASM38214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:37,999] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:38,003] [INFO] Selected 15 target genomes.
[2024-01-24 12:22:38,003] [INFO] Target genome list was writen to GCF_000382145.1_ASM38214v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:38,022] [INFO] Task started: fastANI
[2024-01-24 12:22:38,023] [INFO] Running command: fastANI --query /var/lib/cwl/stge7391ed8-0b8a-4e0e-a8ed-b358d0124744/GCF_000382145.1_ASM38214v1_genomic.fna.gz --refList GCF_000382145.1_ASM38214v1_genomic.fna/target_genomes.txt --output GCF_000382145.1_ASM38214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:47,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:47,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:47,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:47,080] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:47,080] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:47,080] [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
Psychrobacter lutiphocae	strain=DSM 21542	GCA_000382145.1	540500	540500	type	True	100.0	1014	1017	95	conclusive
Psychrobacter phenylpyruvicus	strain=NCTC10526	GCA_900455955.1	29432	29432	type	True	79.4815	322	1017	95	below_threshold
Psychrobacter phenylpyruvicus	strain=DSM 7000	GCA_000685805.1	29432	29432	type	True	79.3362	324	1017	95	below_threshold
Psychrobacter phenylpyruvicus	strain=NBRC 102152	GCA_001591185.1	29432	29432	type	True	79.2504	306	1017	95	below_threshold
Psychrobacter sanguinis	strain=FDAARGOS_1598	GCA_020736705.1	861445	861445	type	True	79.0872	312	1017	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	77.4349	127	1017	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	77.1743	146	1017	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	77.1546	124	1017	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	77.0226	115	1017	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	76.9357	143	1017	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	76.8311	112	1017	95	below_threshold
Moraxella boevrei	strain=DSM 14165	GCA_000379845.1	346665	346665	type	True	76.4217	51	1017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:47,082] [INFO] DFAST Taxonomy check result was written to GCF_000382145.1_ASM38214v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:47,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:47,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:47,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference/checkm_data
[2024-01-24 12:22:47,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:47,118] [INFO] Task started: CheckM
[2024-01-24 12:22:47,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382145.1_ASM38214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382145.1_ASM38214v1_genomic.fna/checkm_input GCF_000382145.1_ASM38214v1_genomic.fna/checkm_result
[2024-01-24 12:23:14,206] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:14,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:14,307] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:14,307] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:14,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382145.1_ASM38214v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:14,308] [INFO] Task started: Blastn
[2024-01-24 12:23:14,308] [INFO] Running command: blastn -query GCF_000382145.1_ASM38214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge31f0319-21d8-48bc-8506-9fef132d6d36/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382145.1_ASM38214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:15,128] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:15,135] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:15,135] [INFO] Target genome list was writen to GCF_000382145.1_ASM38214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:15,147] [INFO] Task started: fastANI
[2024-01-24 12:23:15,147] [INFO] Running command: fastANI --query /var/lib/cwl/stge7391ed8-0b8a-4e0e-a8ed-b358d0124744/GCF_000382145.1_ASM38214v1_genomic.fna.gz --refList GCF_000382145.1_ASM38214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382145.1_ASM38214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:23,460] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:23,471] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:23,471] [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_000382145.1	s__Psychrobacter lutiphocae	100.0	1014	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.95	99.95	0.98	0.98	2	conclusive
GCF_002313155.2	s__Psychrobacter sp002313155	80.505	547	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162815.1	s__Psychrobacter pasteurii	79.3543	330	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685805.1	s__Psychrobacter phenylpyruvicus	79.3249	324	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	99.99	1.00	0.99	4	-
GCF_009725675.1	s__Psychrobacter sanguinis_A	79.3155	339	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.56	98.43	0.91	0.90	4	-
GCF_900162825.1	s__Psychrobacter piechaudii	79.2702	291	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846495.1	s__Psychrobacter sanguinis	79.0905	294	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.88	96.57	0.90	0.89	7	-
GCA_002385225.1	s__Psychrobacter sp002385225	78.8441	308	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260445.1	s__Psychrobacter sp018260445	77.2636	132	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846415.1	s__Psychrobacter piscatorii_A	76.8819	139	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101915.1	s__Psychrobacter pacificensis	76.8592	113	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCF_000379845.1	s__Moraxella_A boevrei	76.4217	51	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,473] [INFO] GTDB search result was written to GCF_000382145.1_ASM38214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:23,473] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:23,479] [INFO] DFAST_QC result json was written to GCF_000382145.1_ASM38214v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:23,479] [INFO] DFAST_QC completed!
[2024-01-24 12:23:23,480] [INFO] Total running time: 0h0m55s