[2024-01-24 14:55:26,017] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference
[2024-01-24 14:55:27,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:27,422] [INFO] Task started: Prodigal
[2024-01-24 14:55:27,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e182cac-ff09-402c-a93a-823ef2df2ad2/GCF_017498075.1_ASM1749807v1_genomic.fna.gz | prodigal -d GCF_017498075.1_ASM1749807v1_genomic.fna/cds.fna -a GCF_017498075.1_ASM1749807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:35,101] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:35,102] [INFO] Task started: HMMsearch
[2024-01-24 14:55:35,102] [INFO] Running command: hmmsearch --tblout GCF_017498075.1_ASM1749807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference/reference_markers.hmm GCF_017498075.1_ASM1749807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:35,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:35,337] [INFO] Found 6/6 markers.
[2024-01-24 14:55:35,363] [INFO] Query marker FASTA was written to GCF_017498075.1_ASM1749807v1_genomic.fna/markers.fasta
[2024-01-24 14:55:35,363] [INFO] Task started: Blastn
[2024-01-24 14:55:35,363] [INFO] Running command: blastn -query GCF_017498075.1_ASM1749807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference/reference_markers.fasta -out GCF_017498075.1_ASM1749807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:36,063] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:36,066] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:36,067] [INFO] Target genome list was writen to GCF_017498075.1_ASM1749807v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:36,096] [INFO] Task started: fastANI
[2024-01-24 14:55:36,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e182cac-ff09-402c-a93a-823ef2df2ad2/GCF_017498075.1_ASM1749807v1_genomic.fna.gz --refList GCF_017498075.1_ASM1749807v1_genomic.fna/target_genomes.txt --output GCF_017498075.1_ASM1749807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:45,572] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:45,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:45,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:45,583] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:45,583] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:55:45,583] [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 halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	100.0	947	948	95	inconclusive
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	95.7299	817	948	95	inconclusive
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	81.2087	564	948	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	80.8384	574	948	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.7606	568	948	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	80.6063	625	948	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	80.4999	594	948	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	80.4834	608	948	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.4509	560	948	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	80.4057	504	948	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	80.0026	591	948	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	79.8935	552	948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:45,585] [INFO] DFAST Taxonomy check result was written to GCF_017498075.1_ASM1749807v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:45,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:45,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:45,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference/checkm_data
[2024-01-24 14:55:45,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:45,618] [INFO] Task started: CheckM
[2024-01-24 14:55:45,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017498075.1_ASM1749807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017498075.1_ASM1749807v1_genomic.fna/checkm_input GCF_017498075.1_ASM1749807v1_genomic.fna/checkm_result
[2024-01-24 14:56:13,156] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:13,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:13,178] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:13,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:13,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017498075.1_ASM1749807v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:13,179] [INFO] Task started: Blastn
[2024-01-24 14:56:13,179] [INFO] Running command: blastn -query GCF_017498075.1_ASM1749807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92fedb7f-8546-45e0-8954-01acb087d232/dqc_reference/reference_markers_gtdb.fasta -out GCF_017498075.1_ASM1749807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:14,314] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:14,318] [INFO] Selected 24 target genomes.
[2024-01-24 14:56:14,318] [INFO] Target genome list was writen to GCF_017498075.1_ASM1749807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:14,339] [INFO] Task started: fastANI
[2024-01-24 14:56:14,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e182cac-ff09-402c-a93a-823ef2df2ad2/GCF_017498075.1_ASM1749807v1_genomic.fna.gz --refList GCF_017498075.1_ASM1749807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017498075.1_ASM1749807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:29,662] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:29,681] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:29,681] [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_016107555.1	s__Psychrobacter celer	95.7038	818	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.12	95.68	0.88	0.85	9	conclusive
GCF_001921745.1	s__Psychrobacter sp001921745	81.7024	534	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.15	99.15	0.97	0.97	2	-
GCF_900101915.1	s__Psychrobacter pacificensis	81.2038	565	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCF_016107575.1	s__Psychrobacter faecalis	80.8381	574	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.81	95.77	0.89	0.85	16	-
GCF_001444505.1	s__Psychrobacter piscatorii	80.6687	548	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	97.27	96.69	0.93	0.91	3	-
GCF_014897815.1	s__Psychrobacter sp003530515	80.6297	623	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2297	99.71	99.49	0.97	0.96	4	-
GCA_002414005.1	s__Psychrobacter sp002414005	80.6053	553	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846075.1	s__Psychrobacter glacincola_C	80.5428	639	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCF_016107545.1	s__Psychrobacter namhaensis	80.4464	559	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.25	97.66	0.93	0.91	5	-
GCF_904846235.1	s__Psychrobacter immobilis_C	80.4293	543	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498085.1	s__Psychrobacter sp017498085	80.4228	502	948	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	80.3278	596	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.29	97.15	0.88	0.85	12	-
GCF_013414195.1	s__Psychrobacter sp013414195	80.2674	549	948	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	80.2568	542	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.96	95.05	0.93	0.86	11	-
GCA_002377945.1	s__Psychrobacter sp002377945	80.2469	552	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836715.1	s__Psychrobacter sp002836715	80.2389	551	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350005.1	s__Psychrobacter proteolyticus_A	80.1745	538	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.98	99.95	0.99	0.99	4	-
GCF_009812035.1	s__Psychrobacter nivimaris_A	80.0388	553	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652895.1	s__Psychrobacter glaciei	80.0026	591	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.25	96.04	0.92	0.86	6	-
GCF_904846155.1	s__Psychrobacter fulvigenes	79.8609	524	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.04	97.04	0.87	0.87	2	-
GCF_900163785.1	s__Psychrobacter alimentarius	79.8328	521	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.11	97.08	0.93	0.93	3	-
GCF_001593285.1	s__Psychrobacter sp001593285	79.7882	497	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.71	97.71	0.93	0.93	2	-
GCF_014861395.1	s__Psychrobacter sp014861395	79.7134	478	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.67	98.67	0.84	0.84	2	-
GCF_001606025.1	s__Psychrobacter alimentarius_A	79.6887	523	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.60	97.20	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:29,683] [INFO] GTDB search result was written to GCF_017498075.1_ASM1749807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:29,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:29,688] [INFO] DFAST_QC result json was written to GCF_017498075.1_ASM1749807v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:29,688] [INFO] DFAST_QC completed!
[2024-01-24 14:56:29,688] [INFO] Total running time: 0h1m4s