[2024-01-24 11:12:26,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:26,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:26,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference
[2024-01-24 11:12:27,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,931] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg65d38479-f35f-48ac-9930-d43b91439f27/GCF_024448735.1_ASM2444873v1_genomic.fna.gz | prodigal -d GCF_024448735.1_ASM2444873v1_genomic.fna/cds.fna -a GCF_024448735.1_ASM2444873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:42,445] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:42,445] [INFO] Task started: HMMsearch
[2024-01-24 11:12:42,445] [INFO] Running command: hmmsearch --tblout GCF_024448735.1_ASM2444873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference/reference_markers.hmm GCF_024448735.1_ASM2444873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:42,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:42,776] [INFO] Found 6/6 markers.
[2024-01-24 11:12:42,817] [INFO] Query marker FASTA was written to GCF_024448735.1_ASM2444873v1_genomic.fna/markers.fasta
[2024-01-24 11:12:42,817] [INFO] Task started: Blastn
[2024-01-24 11:12:42,818] [INFO] Running command: blastn -query GCF_024448735.1_ASM2444873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference/reference_markers.fasta -out GCF_024448735.1_ASM2444873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:43,737] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:43,741] [INFO] Selected 12 target genomes.
[2024-01-24 11:12:43,741] [INFO] Target genome list was writen to GCF_024448735.1_ASM2444873v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:43,746] [INFO] Task started: fastANI
[2024-01-24 11:12:43,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d38479-f35f-48ac-9930-d43b91439f27/GCF_024448735.1_ASM2444873v1_genomic.fna.gz --refList GCF_024448735.1_ASM2444873v1_genomic.fna/target_genomes.txt --output GCF_024448735.1_ASM2444873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:55,083] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:55,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:55,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:55,100] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:55,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:55,101] [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
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	100.0	1537	1539	95	conclusive
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	99.9954	1533	1539	95	conclusive
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	82.3159	964	1539	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	82.212	983	1539	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	80.8851	808	1539	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	80.8537	803	1539	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	80.843	809	1539	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	80.7155	806	1539	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	80.7075	821	1539	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	80.0995	741	1539	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	79.0687	451	1539	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	78.8775	511	1539	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:55,103] [INFO] DFAST Taxonomy check result was written to GCF_024448735.1_ASM2444873v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:55,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:55,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:55,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference/checkm_data
[2024-01-24 11:12:55,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:55,161] [INFO] Task started: CheckM
[2024-01-24 11:12:55,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024448735.1_ASM2444873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024448735.1_ASM2444873v1_genomic.fna/checkm_input GCF_024448735.1_ASM2444873v1_genomic.fna/checkm_result
[2024-01-24 11:13:38,517] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:38,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:38,538] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:38,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:38,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024448735.1_ASM2444873v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:38,540] [INFO] Task started: Blastn
[2024-01-24 11:13:38,540] [INFO] Running command: blastn -query GCF_024448735.1_ASM2444873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8b64fb-2d68-4400-960a-98eee04da619/dqc_reference/reference_markers_gtdb.fasta -out GCF_024448735.1_ASM2444873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:40,153] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:40,157] [INFO] Selected 17 target genomes.
[2024-01-24 11:13:40,157] [INFO] Target genome list was writen to GCF_024448735.1_ASM2444873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:40,171] [INFO] Task started: fastANI
[2024-01-24 11:13:40,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d38479-f35f-48ac-9930-d43b91439f27/GCF_024448735.1_ASM2444873v1_genomic.fna.gz --refList GCF_024448735.1_ASM2444873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024448735.1_ASM2444873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:57,979] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:57,999] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:57,999] [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_003696365.1	s__Pseudomonas_A zhaodongensis	99.9954	1533	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002476945.1	s__Pseudomonas_A stutzeri_Q	85.5867	1309	1539	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	82.5661	981	1539	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	82.5594	1053	1539	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_900129835.1	s__Pseudomonas_A xanthomarina	82.3116	964	1539	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_018138085.1	s__Pseudomonas_A stutzeri_AI	82.1421	1041	1539	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_000952685.1	s__Pseudomonas_A stutzeri_E	82.1285	1066	1539	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	82.126	1005	1539	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_002890895.1	s__Pseudomonas_A stutzeri_AB	82.1147	1035	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCF_003325755.1	s__Pseudomonas_A sp003325755	82.0554	998	1539	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_003527165.1	s__Pseudomonas_A sp003527165	81.9658	559	1539	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	81.8169	946	1539	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	81.8143	948	1539	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_009789555.1	s__Pseudomonas_A stutzeri_R	81.7968	923	1539	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_005876855.1	s__Pseudomonas_R nosocomialis	80.08	744	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCA_900766265.1	s__Pseudomonas_R sp900766265	79.8678	689	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013522725.1	s__Pseudomonas_R azotifigens_A	79.8093	695	1539	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:58,001] [INFO] GTDB search result was written to GCF_024448735.1_ASM2444873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:58,001] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:58,005] [INFO] DFAST_QC result json was written to GCF_024448735.1_ASM2444873v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:58,005] [INFO] DFAST_QC completed!
[2024-01-24 11:13:58,005] [INFO] Total running time: 0h1m31s