[2023-06-26 23:15:42,513] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:15:42,515] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:15:42,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference
[2023-06-26 23:15:43,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:15:43,648] [INFO] Task started: Prodigal
[2023-06-26 23:15:43,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f22dc71-ef07-4cf3-b58a-c06ddad4eb11/GCA_002321095.1_ASM232109v1_genomic.fna.gz | prodigal -d GCA_002321095.1_ASM232109v1_genomic.fna/cds.fna -a GCA_002321095.1_ASM232109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:15:52,460] [INFO] Task succeeded: Prodigal
[2023-06-26 23:15:52,461] [INFO] Task started: HMMsearch
[2023-06-26 23:15:52,461] [INFO] Running command: hmmsearch --tblout GCA_002321095.1_ASM232109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference/reference_markers.hmm GCA_002321095.1_ASM232109v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:15:52,668] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:15:52,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f22dc71-ef07-4cf3-b58a-c06ddad4eb11/GCA_002321095.1_ASM232109v1_genomic.fna.gz]
[2023-06-26 23:15:52,704] [INFO] Query marker FASTA was written to GCA_002321095.1_ASM232109v1_genomic.fna/markers.fasta
[2023-06-26 23:15:52,704] [INFO] Task started: Blastn
[2023-06-26 23:15:52,704] [INFO] Running command: blastn -query GCA_002321095.1_ASM232109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference/reference_markers.fasta -out GCA_002321095.1_ASM232109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:15:53,638] [INFO] Task succeeded: Blastn
[2023-06-26 23:15:53,641] [INFO] Selected 10 target genomes.
[2023-06-26 23:15:53,641] [INFO] Target genome list was writen to GCA_002321095.1_ASM232109v1_genomic.fna/target_genomes.txt
[2023-06-26 23:15:53,642] [INFO] Task started: fastANI
[2023-06-26 23:15:53,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f22dc71-ef07-4cf3-b58a-c06ddad4eb11/GCA_002321095.1_ASM232109v1_genomic.fna.gz --refList GCA_002321095.1_ASM232109v1_genomic.fna/target_genomes.txt --output GCA_002321095.1_ASM232109v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:16:02,695] [INFO] Task succeeded: fastANI
[2023-06-26 23:16:02,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:16:02,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:16:02,703] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-26 23:16:02,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-26 23:16:02,703] [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
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	98.0624	1064	1113	95	conclusive
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	98.0519	1065	1113	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	91.2132	973	1113	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	91.1597	975	1113	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	91.1133	964	1113	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	89.0927	966	1113	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	89.0417	979	1113	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.1044	756	1113	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	82.5847	747	1113	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	80.8494	552	1113	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:16:02,705] [INFO] DFAST Taxonomy check result was written to GCA_002321095.1_ASM232109v1_genomic.fna/tc_result.tsv
[2023-06-26 23:16:02,705] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:16:02,705] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:16:02,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference/checkm_data
[2023-06-26 23:16:02,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:16:02,745] [INFO] Task started: CheckM
[2023-06-26 23:16:02,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002321095.1_ASM232109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002321095.1_ASM232109v1_genomic.fna/checkm_input GCA_002321095.1_ASM232109v1_genomic.fna/checkm_result
[2023-06-26 23:16:29,922] [INFO] Task succeeded: CheckM
[2023-06-26 23:16:29,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:16:29,939] [INFO] ===== Completeness check finished =====
[2023-06-26 23:16:29,939] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:16:29,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002321095.1_ASM232109v1_genomic.fna/markers.fasta)
[2023-06-26 23:16:29,942] [INFO] Task started: Blastn
[2023-06-26 23:16:29,942] [INFO] Running command: blastn -query GCA_002321095.1_ASM232109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b60aa44-4bbf-4025-a142-abcc38e06e62/dqc_reference/reference_markers_gtdb.fasta -out GCA_002321095.1_ASM232109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:16:31,671] [INFO] Task succeeded: Blastn
[2023-06-26 23:16:31,674] [INFO] Selected 11 target genomes.
[2023-06-26 23:16:31,674] [INFO] Target genome list was writen to GCA_002321095.1_ASM232109v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:16:31,679] [INFO] Task started: fastANI
[2023-06-26 23:16:31,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f22dc71-ef07-4cf3-b58a-c06ddad4eb11/GCA_002321095.1_ASM232109v1_genomic.fna.gz --refList GCA_002321095.1_ASM232109v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002321095.1_ASM232109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:16:42,966] [INFO] Task succeeded: fastANI
[2023-06-26 23:16:42,974] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:16:42,974] [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_000219605.1	s__Pseudomonas_A stutzeri	98.0624	1064	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	conclusive
GCF_003205815.1	s__Pseudomonas_A sp003205815	90.6628	971	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	89.0268	980	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	87.6531	974	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0711	97.19	97.19	0.89	0.89	2	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	87.6161	984	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	87.4744	962	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.44	99.44	0.92	0.92	2	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	87.4367	912	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	86.9408	904	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	86.6011	906	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_002890795.1	s__Pseudomonas_A stutzeri_AA	85.9506	958	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.7879	875	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-26 23:16:42,976] [INFO] GTDB search result was written to GCA_002321095.1_ASM232109v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:16:42,976] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:16:42,979] [INFO] DFAST_QC result json was written to GCA_002321095.1_ASM232109v1_genomic.fna/dqc_result.json
[2023-06-26 23:16:42,979] [INFO] DFAST_QC completed!
[2023-06-26 23:16:42,979] [INFO] Total running time: 0h1m0s