[2024-01-24 13:22:00,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference
[2024-01-24 13:22:02,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,424] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg68438663-6795-4974-9f60-c07a8960c444/GCF_012986195.1_ASM1298619v1_genomic.fna.gz | prodigal -d GCF_012986195.1_ASM1298619v1_genomic.fna/cds.fna -a GCF_012986195.1_ASM1298619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:17,806] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:17,806] [INFO] Task started: HMMsearch
[2024-01-24 13:22:17,807] [INFO] Running command: hmmsearch --tblout GCF_012986195.1_ASM1298619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference/reference_markers.hmm GCF_012986195.1_ASM1298619v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:18,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:18,168] [INFO] Found 6/6 markers.
[2024-01-24 13:22:18,212] [INFO] Query marker FASTA was written to GCF_012986195.1_ASM1298619v1_genomic.fna/markers.fasta
[2024-01-24 13:22:18,213] [INFO] Task started: Blastn
[2024-01-24 13:22:18,213] [INFO] Running command: blastn -query GCF_012986195.1_ASM1298619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference/reference_markers.fasta -out GCF_012986195.1_ASM1298619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:19,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:19,321] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:19,321] [INFO] Target genome list was writen to GCF_012986195.1_ASM1298619v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:19,353] [INFO] Task started: fastANI
[2024-01-24 13:22:19,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg68438663-6795-4974-9f60-c07a8960c444/GCF_012986195.1_ASM1298619v1_genomic.fna.gz --refList GCF_012986195.1_ASM1298619v1_genomic.fna/target_genomes.txt --output GCF_012986195.1_ASM1298619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:36,978] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:36,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:36,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:36,991] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:36,992] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:36,992] [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 oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	100.0	1672	1673	95	inconclusive
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	99.9882	1654	1673	95	inconclusive
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	98.3987	1536	1673	95	inconclusive
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	98.3875	1541	1673	95	inconclusive
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	89.7689	1422	1673	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	80.8362	664	1673	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	80.8272	616	1673	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	80.5128	673	1673	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.4867	704	1673	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.1741	645	1673	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.0798	647	1673	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	79.8963	571	1673	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	79.892	618	1673	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	79.7976	613	1673	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	78.9944	566	1673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,994] [INFO] DFAST Taxonomy check result was written to GCF_012986195.1_ASM1298619v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:36,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:36,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:36,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference/checkm_data
[2024-01-24 13:22:36,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:37,050] [INFO] Task started: CheckM
[2024-01-24 13:22:37,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012986195.1_ASM1298619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012986195.1_ASM1298619v1_genomic.fna/checkm_input GCF_012986195.1_ASM1298619v1_genomic.fna/checkm_result
[2024-01-24 13:23:22,533] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:22,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:22,554] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:22,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:22,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012986195.1_ASM1298619v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:22,555] [INFO] Task started: Blastn
[2024-01-24 13:23:22,555] [INFO] Running command: blastn -query GCF_012986195.1_ASM1298619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b79650-0766-41b9-b026-0d5b9017f8e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012986195.1_ASM1298619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:24,442] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:24,446] [INFO] Selected 9 target genomes.
[2024-01-24 13:23:24,446] [INFO] Target genome list was writen to GCF_012986195.1_ASM1298619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:24,466] [INFO] Task started: fastANI
[2024-01-24 13:23:24,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg68438663-6795-4974-9f60-c07a8960c444/GCF_012986195.1_ASM1298619v1_genomic.fna.gz --refList GCF_012986195.1_ASM1298619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012986195.1_ASM1298619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:37,685] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:37,696] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:37,696] [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_000730625.1	s__Pseudomonas_B oryzihabitans	99.9882	1654	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.97	96.38	0.92	0.87	28	conclusive
GCF_014522265.1	s__Pseudomonas_B oryzihabitans_D	93.7944	1506	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	96.63	95.05	0.89	0.84	6	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	93.0727	1432	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_001518815.1	s__Pseudomonas_B oryzihabitans_E	91.2137	1422	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_007665395.1	s__Pseudomonas_B psychrotolerans_C	91.0543	1447	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	90.4592	1421	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005250615.1	s__Pseudomonas_B rhizoryzae	89.7757	1421	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.30	97.74	0.93	0.89	15	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	89.7032	1372	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498575.2	s__Pseudomonas_E taeanensis	78.8124	510	1673	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:37,698] [INFO] GTDB search result was written to GCF_012986195.1_ASM1298619v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:37,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:37,702] [INFO] DFAST_QC result json was written to GCF_012986195.1_ASM1298619v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:37,702] [INFO] DFAST_QC completed!
[2024-01-24 13:23:37,702] [INFO] Total running time: 0h1m37s