[2024-01-24 11:44:05,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,457] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference
[2024-01-24 11:44:08,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,841] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,841] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f689934-9623-471b-848d-eef305174696/GCF_003217155.1_ASM321715v1_genomic.fna.gz | prodigal -d GCF_003217155.1_ASM321715v1_genomic.fna/cds.fna -a GCF_003217155.1_ASM321715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:16,783] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:16,783] [INFO] Task started: HMMsearch
[2024-01-24 11:44:16,784] [INFO] Running command: hmmsearch --tblout GCF_003217155.1_ASM321715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference/reference_markers.hmm GCF_003217155.1_ASM321715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:17,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:17,069] [INFO] Found 6/6 markers.
[2024-01-24 11:44:17,098] [INFO] Query marker FASTA was written to GCF_003217155.1_ASM321715v1_genomic.fna/markers.fasta
[2024-01-24 11:44:17,099] [INFO] Task started: Blastn
[2024-01-24 11:44:17,099] [INFO] Running command: blastn -query GCF_003217155.1_ASM321715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference/reference_markers.fasta -out GCF_003217155.1_ASM321715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:17,760] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:17,764] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:17,764] [INFO] Target genome list was writen to GCF_003217155.1_ASM321715v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:17,799] [INFO] Task started: fastANI
[2024-01-24 11:44:17,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f689934-9623-471b-848d-eef305174696/GCF_003217155.1_ASM321715v1_genomic.fna.gz --refList GCF_003217155.1_ASM321715v1_genomic.fna/target_genomes.txt --output GCF_003217155.1_ASM321715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:27,273] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:27,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:27,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:27,285] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:27,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:27,285] [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 fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	100.0	1153	1154	95	conclusive
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	83.1828	755	1154	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	82.7824	764	1154	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	82.6641	754	1154	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	82.4681	756	1154	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	81.3602	664	1154	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	81.1251	639	1154	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	80.7752	609	1154	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.2945	560	1154	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	79.9955	552	1154	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	79.8176	566	1154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:27,287] [INFO] DFAST Taxonomy check result was written to GCF_003217155.1_ASM321715v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:27,287] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:27,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:27,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference/checkm_data
[2024-01-24 11:44:27,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:27,327] [INFO] Task started: CheckM
[2024-01-24 11:44:27,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217155.1_ASM321715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217155.1_ASM321715v1_genomic.fna/checkm_input GCF_003217155.1_ASM321715v1_genomic.fna/checkm_result
[2024-01-24 11:44:56,970] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:56,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:56,991] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:56,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:56,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217155.1_ASM321715v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:56,992] [INFO] Task started: Blastn
[2024-01-24 11:44:56,993] [INFO] Running command: blastn -query GCF_003217155.1_ASM321715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4ab5d73-cb0b-4312-bb8d-433667dee45c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217155.1_ASM321715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:58,056] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:58,060] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:58,061] [INFO] Target genome list was writen to GCF_003217155.1_ASM321715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:58,071] [INFO] Task started: fastANI
[2024-01-24 11:44:58,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f689934-9623-471b-848d-eef305174696/GCF_003217155.1_ASM321715v1_genomic.fna.gz --refList GCF_003217155.1_ASM321715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217155.1_ASM321715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:08,941] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:08,963] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:08,964] [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_003217155.1	s__Psychrobacter fozii	100.0	1153	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.56	95.06	0.91	0.88	5	conclusive
GCF_015234355.1	s__Psychrobacter sp015234355	93.4688	1016	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015864825.1	s__Psychrobacter sp015864825	92.5364	1001	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277735.1	s__Psychrobacter sp015277735	84.7922	802	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.26	95.15	0.92	0.92	3	-
GCF_014861395.1	s__Psychrobacter sp014861395	83.977	760	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.67	98.67	0.84	0.84	2	-
GCF_014652895.1	s__Psychrobacter glaciei	83.2127	751	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.25	96.04	0.92	0.86	6	-
GCF_002836735.1	s__Psychrobacter sp002836735	82.8971	724	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_904846075.1	s__Psychrobacter glacincola_C	82.7057	792	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCF_002836715.1	s__Psychrobacter sp002836715	82.6255	711	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014897815.1	s__Psychrobacter sp003530515	82.5996	773	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2297	99.71	99.49	0.97	0.96	4	-
GCF_002836505.1	s__Psychrobacter sp002836505	82.5945	740	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.96	95.05	0.93	0.86	11	-
GCF_016107525.1	s__Psychrobacter aquimaris	82.438	758	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.04	97.20	0.92	0.89	5	-
GCF_008369115.1	s__Psychrobacter sp008369115	80.7021	604	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:08,967] [INFO] GTDB search result was written to GCF_003217155.1_ASM321715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:08,968] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:08,972] [INFO] DFAST_QC result json was written to GCF_003217155.1_ASM321715v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:08,972] [INFO] DFAST_QC completed!
[2024-01-24 11:45:08,972] [INFO] Total running time: 0h1m4s