[2024-01-24 12:52:25,703] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:25,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:25,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference
[2024-01-24 12:52:27,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:27,010] [INFO] Task started: Prodigal
[2024-01-24 12:52:27,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eb5eb14-4efe-41c8-b8c1-8c3ca6acbcae/GCF_024328335.1_ASM2432833v1_genomic.fna.gz | prodigal -d GCF_024328335.1_ASM2432833v1_genomic.fna/cds.fna -a GCF_024328335.1_ASM2432833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:40,010] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:40,010] [INFO] Task started: HMMsearch
[2024-01-24 12:52:40,010] [INFO] Running command: hmmsearch --tblout GCF_024328335.1_ASM2432833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference/reference_markers.hmm GCF_024328335.1_ASM2432833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:40,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:40,333] [INFO] Found 6/6 markers.
[2024-01-24 12:52:40,381] [INFO] Query marker FASTA was written to GCF_024328335.1_ASM2432833v1_genomic.fna/markers.fasta
[2024-01-24 12:52:40,381] [INFO] Task started: Blastn
[2024-01-24 12:52:40,381] [INFO] Running command: blastn -query GCF_024328335.1_ASM2432833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference/reference_markers.fasta -out GCF_024328335.1_ASM2432833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:41,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:41,483] [INFO] Selected 12 target genomes.
[2024-01-24 12:52:41,484] [INFO] Target genome list was writen to GCF_024328335.1_ASM2432833v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:41,490] [INFO] Task started: fastANI
[2024-01-24 12:52:41,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb5eb14-4efe-41c8-b8c1-8c3ca6acbcae/GCF_024328335.1_ASM2432833v1_genomic.fna.gz --refList GCF_024328335.1_ASM2432833v1_genomic.fna/target_genomes.txt --output GCF_024328335.1_ASM2432833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:53,731] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:53,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:53,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:53,747] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:52:53,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:53,747] [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	100.0	1411	1413	95	conclusive
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	99.9986	1413	1413	95	conclusive
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	82.3035	955	1413	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	82.2948	944	1413	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	81.6474	839	1413	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	81.4726	829	1413	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	81.3144	784	1413	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.2655	790	1413	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.24	807	1413	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.2142	871	1413	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	80.6523	733	1413	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	79.3838	570	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:53,749] [INFO] DFAST Taxonomy check result was written to GCF_024328335.1_ASM2432833v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:53,750] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:53,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:53,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference/checkm_data
[2024-01-24 12:52:53,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:53,794] [INFO] Task started: CheckM
[2024-01-24 12:52:53,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024328335.1_ASM2432833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024328335.1_ASM2432833v1_genomic.fna/checkm_input GCF_024328335.1_ASM2432833v1_genomic.fna/checkm_result
[2024-01-24 12:53:33,802] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:33,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:33,827] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:33,828] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:33,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024328335.1_ASM2432833v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:33,829] [INFO] Task started: Blastn
[2024-01-24 12:53:33,829] [INFO] Running command: blastn -query GCF_024328335.1_ASM2432833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ae8354-d36d-4941-9e63-4553f7b6b96a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024328335.1_ASM2432833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:35,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:35,507] [INFO] Selected 13 target genomes.
[2024-01-24 12:53:35,507] [INFO] Target genome list was writen to GCF_024328335.1_ASM2432833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:35,525] [INFO] Task started: fastANI
[2024-01-24 12:53:35,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb5eb14-4efe-41c8-b8c1-8c3ca6acbcae/GCF_024328335.1_ASM2432833v1_genomic.fna.gz --refList GCF_024328335.1_ASM2432833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024328335.1_ASM2432833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:49,260] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:49,271] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:49,271] [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_900129835.1	s__Pseudomonas_A xanthomarina	99.9986	1413	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	91.7873	1135	1413	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	88.222	1230	1413	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_002890895.1	s__Pseudomonas_A stutzeri_AB	88.2183	1203	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCA_002452485.1	s__Pseudomonas_A stutzeri_P	84.5183	1021	1413	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	83.291	1051	1413	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_002387205.1	s__Pseudomonas_A stutzeri_N	83.2567	966	1413	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_018138085.1	s__Pseudomonas_A stutzeri_AI	83.2134	1088	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCF_013620795.1	s__Pseudomonas_A sp013620795	83.1899	1021	1413	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	82.8307	1019	1413	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_002339675.1	s__Pseudomonas_A stutzeri_O	82.7883	1033	1413	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_009789555.1	s__Pseudomonas_A stutzeri_R	82.4599	985	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
GCF_003696365.1	s__Pseudomonas_A zhaodongensis	82.3118	954	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:49,273] [INFO] GTDB search result was written to GCF_024328335.1_ASM2432833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:49,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:49,277] [INFO] DFAST_QC result json was written to GCF_024328335.1_ASM2432833v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:49,278] [INFO] DFAST_QC completed!
[2024-01-24 12:53:49,278] [INFO] Total running time: 0h1m24s