[2024-01-25 17:34:07,126] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference
[2024-01-25 17:34:09,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,027] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,027] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdf2f13a-051a-4683-9061-5835644ec653/GCF_016107545.1_ASM1610754v1_genomic.fna.gz | prodigal -d GCF_016107545.1_ASM1610754v1_genomic.fna/cds.fna -a GCF_016107545.1_ASM1610754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:15,238] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:15,239] [INFO] Task started: HMMsearch
[2024-01-25 17:34:15,239] [INFO] Running command: hmmsearch --tblout GCF_016107545.1_ASM1610754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference/reference_markers.hmm GCF_016107545.1_ASM1610754v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:15,493] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:15,494] [INFO] Found 6/6 markers.
[2024-01-25 17:34:15,517] [INFO] Query marker FASTA was written to GCF_016107545.1_ASM1610754v1_genomic.fna/markers.fasta
[2024-01-25 17:34:15,517] [INFO] Task started: Blastn
[2024-01-25 17:34:15,517] [INFO] Running command: blastn -query GCF_016107545.1_ASM1610754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference/reference_markers.fasta -out GCF_016107545.1_ASM1610754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:16,113] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:16,115] [INFO] Selected 20 target genomes.
[2024-01-25 17:34:16,116] [INFO] Target genome list was writen to GCF_016107545.1_ASM1610754v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:16,132] [INFO] Task started: fastANI
[2024-01-25 17:34:16,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdf2f13a-051a-4683-9061-5835644ec653/GCF_016107545.1_ASM1610754v1_genomic.fna.gz --refList GCF_016107545.1_ASM1610754v1_genomic.fna/target_genomes.txt --output GCF_016107545.1_ASM1610754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:30,252] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:30,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:30,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:30,262] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:30,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:30,263] [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 namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	100.0	945	946	95	conclusive
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	83.3562	737	946	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	82.3109	726	946	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	82.2019	715	946	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	81.9489	688	946	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	81.4811	629	946	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	81.3518	672	946	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	81.2416	662	946	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.8872	584	946	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	80.586	580	946	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.55	598	946	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	80.4574	541	946	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	80.4524	581	946	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	80.3108	568	946	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	78.734	398	946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:30,264] [INFO] DFAST Taxonomy check result was written to GCF_016107545.1_ASM1610754v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:30,264] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:30,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:30,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference/checkm_data
[2024-01-25 17:34:30,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:30,295] [INFO] Task started: CheckM
[2024-01-25 17:34:30,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016107545.1_ASM1610754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016107545.1_ASM1610754v1_genomic.fna/checkm_input GCF_016107545.1_ASM1610754v1_genomic.fna/checkm_result
[2024-01-25 17:34:53,425] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:53,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:53,443] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:53,444] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:53,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016107545.1_ASM1610754v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:53,444] [INFO] Task started: Blastn
[2024-01-25 17:34:53,444] [INFO] Running command: blastn -query GCF_016107545.1_ASM1610754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f0acb55-1bc7-4eba-b722-e1d8857b74cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_016107545.1_ASM1610754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:54,388] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:54,391] [INFO] Selected 28 target genomes.
[2024-01-25 17:34:54,391] [INFO] Target genome list was writen to GCF_016107545.1_ASM1610754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:34:54,409] [INFO] Task started: fastANI
[2024-01-25 17:34:54,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdf2f13a-051a-4683-9061-5835644ec653/GCF_016107545.1_ASM1610754v1_genomic.fna.gz --refList GCF_016107545.1_ASM1610754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016107545.1_ASM1610754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:13,270] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:13,284] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:13,284] [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_016107545.1	s__Psychrobacter namhaensis	100.0	945	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.25	97.66	0.93	0.91	5	conclusive
GCF_904846715.1	s__Psychrobacter vallis	83.4139	741	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000471625.1	s__Psychrobacter aquaticus	83.3653	736	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846225.1	s__Psychrobacter immobilis_F	82.7062	739	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107525.1	s__Psychrobacter aquimaris	82.3138	725	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.04	97.20	0.92	0.89	5	-
GCF_001606025.1	s__Psychrobacter alimentarius_A	82.091	715	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.60	97.20	0.95	0.90	3	-
GCF_904846235.1	s__Psychrobacter immobilis_C	81.589	646	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836505.1	s__Psychrobacter sp002836505	81.588	647	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.96	95.05	0.93	0.86	11	-
GCF_002836715.1	s__Psychrobacter sp002836715	81.5544	625	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435845.1	s__Psychrobacter sp001435845	81.5204	636	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836735.1	s__Psychrobacter sp002836735	81.4805	645	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_900101915.1	s__Psychrobacter pacificensis	81.4786	630	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCF_904846705.1	s__Psychrobacter sp904846705	81.4048	633	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846625.1	s__Psychrobacter sp000586415	81.3805	659	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.91	99.91	1.00	1.00	2	-
GCF_904846415.1	s__Psychrobacter piscatorii_A	81.3578	652	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014770435.1	s__Psychrobacter sp014770435	81.3455	649	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444505.1	s__Psychrobacter piscatorii	81.2964	620	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	97.27	96.69	0.93	0.91	3	-
GCA_002377945.1	s__Psychrobacter sp002377945	81.2215	638	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107575.1	s__Psychrobacter faecalis	80.5755	581	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.81	95.77	0.89	0.85	16	-
GCA_002414005.1	s__Psychrobacter sp002414005	80.5442	579	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453355.1	s__Psychrobacter sp002453355	80.2432	560	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846675.1	s__Psychrobacter urativorans_B	78.6924	410	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.89	97.89	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:13,286] [INFO] GTDB search result was written to GCF_016107545.1_ASM1610754v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:13,286] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:13,289] [INFO] DFAST_QC result json was written to GCF_016107545.1_ASM1610754v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:13,290] [INFO] DFAST_QC completed!
[2024-01-25 17:35:13,290] [INFO] Total running time: 0h1m6s