[2023-06-19 10:05:30,198] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:05:30,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:05:30,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference
[2023-06-19 10:05:32,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:05:32,060] [INFO] Task started: Prodigal
[2023-06-19 10:05:32,061] [INFO] Running command: gunzip -c /var/lib/cwl/stge2fa5adf-201f-4cad-a97f-7dc826284942/GCA_018820105.1_ASM1882010v1_genomic.fna.gz | prodigal -d GCA_018820105.1_ASM1882010v1_genomic.fna/cds.fna -a GCA_018820105.1_ASM1882010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:05:43,395] [INFO] Task succeeded: Prodigal
[2023-06-19 10:05:43,396] [INFO] Task started: HMMsearch
[2023-06-19 10:05:43,396] [INFO] Running command: hmmsearch --tblout GCA_018820105.1_ASM1882010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference/reference_markers.hmm GCA_018820105.1_ASM1882010v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:05:43,668] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:05:43,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge2fa5adf-201f-4cad-a97f-7dc826284942/GCA_018820105.1_ASM1882010v1_genomic.fna.gz]
[2023-06-19 10:05:43,705] [INFO] Query marker FASTA was written to GCA_018820105.1_ASM1882010v1_genomic.fna/markers.fasta
[2023-06-19 10:05:43,706] [INFO] Task started: Blastn
[2023-06-19 10:05:43,706] [INFO] Running command: blastn -query GCA_018820105.1_ASM1882010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference/reference_markers.fasta -out GCA_018820105.1_ASM1882010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:05:44,570] [INFO] Task succeeded: Blastn
[2023-06-19 10:05:44,574] [INFO] Selected 11 target genomes.
[2023-06-19 10:05:44,575] [INFO] Target genome list was writen to GCA_018820105.1_ASM1882010v1_genomic.fna/target_genomes.txt
[2023-06-19 10:05:44,576] [INFO] Task started: fastANI
[2023-06-19 10:05:44,577] [INFO] Running command: fastANI --query /var/lib/cwl/stge2fa5adf-201f-4cad-a97f-7dc826284942/GCA_018820105.1_ASM1882010v1_genomic.fna.gz --refList GCA_018820105.1_ASM1882010v1_genomic.fna/target_genomes.txt --output GCA_018820105.1_ASM1882010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:05:53,431] [INFO] Task succeeded: fastANI
[2023-06-19 10:05:53,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:05:53,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:05:53,446] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:05:53,446] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:05:53,446] [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 xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	87.9069	1041	1252	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	87.8821	1054	1252	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	81.6928	885	1252	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	81.6669	893	1252	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	81.0022	706	1252	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	80.7627	713	1252	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	80.4871	638	1252	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	80.4725	652	1252	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	80.4642	644	1252	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	80.2355	644	1252	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	79.0823	443	1252	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:05:53,448] [INFO] DFAST Taxonomy check result was written to GCA_018820105.1_ASM1882010v1_genomic.fna/tc_result.tsv
[2023-06-19 10:05:53,449] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:05:53,449] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:05:53,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference/checkm_data
[2023-06-19 10:05:53,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:05:53,488] [INFO] Task started: CheckM
[2023-06-19 10:05:53,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018820105.1_ASM1882010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018820105.1_ASM1882010v1_genomic.fna/checkm_input GCA_018820105.1_ASM1882010v1_genomic.fna/checkm_result
[2023-06-19 10:06:30,448] [INFO] Task succeeded: CheckM
[2023-06-19 10:06:30,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 8.80%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:06:30,475] [INFO] ===== Completeness check finished =====
[2023-06-19 10:06:30,476] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:06:30,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018820105.1_ASM1882010v1_genomic.fna/markers.fasta)
[2023-06-19 10:06:30,476] [INFO] Task started: Blastn
[2023-06-19 10:06:30,476] [INFO] Running command: blastn -query GCA_018820105.1_ASM1882010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd117fc12-d48d-4773-873c-2a48eec256a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018820105.1_ASM1882010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:06:32,084] [INFO] Task succeeded: Blastn
[2023-06-19 10:06:32,108] [INFO] Selected 10 target genomes.
[2023-06-19 10:06:32,109] [INFO] Target genome list was writen to GCA_018820105.1_ASM1882010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:06:32,123] [INFO] Task started: fastANI
[2023-06-19 10:06:32,123] [INFO] Running command: fastANI --query /var/lib/cwl/stge2fa5adf-201f-4cad-a97f-7dc826284942/GCA_018820105.1_ASM1882010v1_genomic.fna.gz --refList GCA_018820105.1_ASM1882010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018820105.1_ASM1882010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:06:42,225] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:42,237] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:06:42,237] [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_002890895.1	s__Pseudomonas_A stutzeri_AB	97.2519	1167	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	conclusive
GCF_900129835.1	s__Pseudomonas_A xanthomarina	87.8821	1054	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	87.7314	988	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004010935.1	s__Pseudomonas_A sp004010935	87.2104	1123	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	96.94	95.82	0.92	0.89	15	-
GCF_018138085.1	s__Pseudomonas_A stutzeri_AI	82.9483	950	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCA_002387205.1	s__Pseudomonas_A stutzeri_N	82.8264	865	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.23	98.23	0.88	0.88	2	-
GCF_019090095.1	s__Pseudomonas_A stutzeri_AN	82.7742	925	1252	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_000590475.1	s__Pseudomonas_A stutzeri_D	82.2799	912	1252	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_003325755.1	s__Pseudomonas_A sp003325755	82.2645	895	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452485.1	s__Pseudomonas_A stutzeri_P	82.0112	861	1252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:06:42,245] [INFO] GTDB search result was written to GCA_018820105.1_ASM1882010v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:06:42,246] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:06:42,250] [INFO] DFAST_QC result json was written to GCA_018820105.1_ASM1882010v1_genomic.fna/dqc_result.json
[2023-06-19 10:06:42,250] [INFO] DFAST_QC completed!
[2023-06-19 10:06:42,250] [INFO] Total running time: 0h1m12s