[2024-01-24 13:46:25,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,953] [INFO] DQC Reference Directory: /var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference
[2024-01-24 13:46:27,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,735] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c07664d-7aed-4c20-84f4-ed70d7d7d4d2/GCF_007997305.1_ASM799730v1_genomic.fna.gz | prodigal -d GCF_007997305.1_ASM799730v1_genomic.fna/cds.fna -a GCF_007997305.1_ASM799730v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:33,169] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:33,170] [INFO] Task started: HMMsearch
[2024-01-24 13:46:33,170] [INFO] Running command: hmmsearch --tblout GCF_007997305.1_ASM799730v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference/reference_markers.hmm GCF_007997305.1_ASM799730v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:33,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:33,446] [INFO] Found 6/6 markers.
[2024-01-24 13:46:33,482] [INFO] Query marker FASTA was written to GCF_007997305.1_ASM799730v1_genomic.fna/markers.fasta
[2024-01-24 13:46:33,482] [INFO] Task started: Blastn
[2024-01-24 13:46:33,482] [INFO] Running command: blastn -query GCF_007997305.1_ASM799730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference/reference_markers.fasta -out GCF_007997305.1_ASM799730v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:34,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:34,124] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:34,125] [INFO] Target genome list was writen to GCF_007997305.1_ASM799730v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:34,174] [INFO] Task started: fastANI
[2024-01-24 13:46:34,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c07664d-7aed-4c20-84f4-ed70d7d7d4d2/GCF_007997305.1_ASM799730v1_genomic.fna.gz --refList GCF_007997305.1_ASM799730v1_genomic.fna/target_genomes.txt --output GCF_007997305.1_ASM799730v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:45,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:45,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:45,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:45,112] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:45,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:45,112] [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 frigidicola	strain=ACAM 304	GCA_007997305.1	45611	45611	type	True	100.0	945	945	95	conclusive
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	79.4098	404	945	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	79.3248	439	945	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	79.1545	430	945	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	79.0631	427	945	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	78.9793	430	945	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	78.9712	394	945	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	78.959	433	945	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	78.9039	410	945	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	78.9025	425	945	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	78.838	448	945	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	78.5839	363	945	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	78.4836	316	945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:45,122] [INFO] DFAST Taxonomy check result was written to GCF_007997305.1_ASM799730v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:45,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:45,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:45,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference/checkm_data
[2024-01-24 13:46:45,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:45,161] [INFO] Task started: CheckM
[2024-01-24 13:46:45,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997305.1_ASM799730v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997305.1_ASM799730v1_genomic.fna/checkm_input GCF_007997305.1_ASM799730v1_genomic.fna/checkm_result
[2024-01-24 13:47:06,799] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:06,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,816] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:06,817] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:06,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997305.1_ASM799730v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:06,817] [INFO] Task started: Blastn
[2024-01-24 13:47:06,817] [INFO] Running command: blastn -query GCF_007997305.1_ASM799730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5816749-7695-4963-8f12-ec666d16d104/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997305.1_ASM799730v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:07,854] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:07,862] [INFO] Selected 13 target genomes.
[2024-01-24 13:47:07,862] [INFO] Target genome list was writen to GCF_007997305.1_ASM799730v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:07,874] [INFO] Task started: fastANI
[2024-01-24 13:47:07,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c07664d-7aed-4c20-84f4-ed70d7d7d4d2/GCF_007997305.1_ASM799730v1_genomic.fna.gz --refList GCF_007997305.1_ASM799730v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997305.1_ASM799730v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:16,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:16,311] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:16,311] [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_007997305.1	s__Psychrobacter frigidicola	100.0	945	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_904846675.1	s__Psychrobacter urativorans_B	82.3125	699	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.89	97.89	0.92	0.92	2	-
GCF_001298525.1	s__Psychrobacter urativorans_A	81.1073	629	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014119005.1	s__Psychrobacter sp014119005	80.4476	559	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875835.1	s__Psychrobacter sp017875835	79.8561	514	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168255.1	s__Psychrobacter sp900168255	79.8312	497	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.48	96.48	0.91	0.91	2	-
GCF_904846605.1	s__Psychrobacter sp904846605	79.7781	540	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846175.1	s__Psychrobacter immobilis_E	79.4462	441	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192115.1	s__Psychrobacter luti	79.3248	439	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008369115.1	s__Psychrobacter sp008369115	79.2539	451	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248965.1	s__Psychrobacter okhotskensis	79.0799	416	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.29	97.15	0.88	0.85	12	-
GCF_014861365.1	s__Psychrobacter sp014861365	78.8452	431	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.77	98.77	0.85	0.85	2	-
GCF_001921745.1	s__Psychrobacter sp001921745	78.3475	397	945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.15	99.15	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:16,312] [INFO] GTDB search result was written to GCF_007997305.1_ASM799730v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:16,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:16,316] [INFO] DFAST_QC result json was written to GCF_007997305.1_ASM799730v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:16,316] [INFO] DFAST_QC completed!
[2024-01-24 13:47:16,316] [INFO] Total running time: 0h0m50s