[2023-06-17 15:46:54,122] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:46:54,127] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:46:54,127] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference
[2023-06-17 15:46:55,474] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:46:55,475] [INFO] Task started: Prodigal
[2023-06-17 15:46:55,475] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf1bb218-29d2-4db8-9602-8c6ba6d7fdc5/GCA_003488145.1_ASM348814v1_genomic.fna.gz | prodigal -d GCA_003488145.1_ASM348814v1_genomic.fna/cds.fna -a GCA_003488145.1_ASM348814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:47:04,452] [INFO] Task succeeded: Prodigal
[2023-06-17 15:47:04,452] [INFO] Task started: HMMsearch
[2023-06-17 15:47:04,452] [INFO] Running command: hmmsearch --tblout GCA_003488145.1_ASM348814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference/reference_markers.hmm GCA_003488145.1_ASM348814v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:47:04,710] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:47:04,711] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaf1bb218-29d2-4db8-9602-8c6ba6d7fdc5/GCA_003488145.1_ASM348814v1_genomic.fna.gz]
[2023-06-17 15:47:04,748] [INFO] Query marker FASTA was written to GCA_003488145.1_ASM348814v1_genomic.fna/markers.fasta
[2023-06-17 15:47:04,749] [INFO] Task started: Blastn
[2023-06-17 15:47:04,749] [INFO] Running command: blastn -query GCA_003488145.1_ASM348814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference/reference_markers.fasta -out GCA_003488145.1_ASM348814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:47:05,653] [INFO] Task succeeded: Blastn
[2023-06-17 15:47:05,657] [INFO] Selected 9 target genomes.
[2023-06-17 15:47:05,658] [INFO] Target genome list was writen to GCA_003488145.1_ASM348814v1_genomic.fna/target_genomes.txt
[2023-06-17 15:47:05,662] [INFO] Task started: fastANI
[2023-06-17 15:47:05,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf1bb218-29d2-4db8-9602-8c6ba6d7fdc5/GCA_003488145.1_ASM348814v1_genomic.fna.gz --refList GCA_003488145.1_ASM348814v1_genomic.fna/target_genomes.txt --output GCA_003488145.1_ASM348814v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:47:14,129] [INFO] Task succeeded: fastANI
[2023-06-17 15:47:14,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:47:14,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:47:14,138] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-17 15:47:14,138] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-17 15:47:14,138] [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 kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	96.5929	856	965	95	inconclusive
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	96.5409	858	965	95	inconclusive
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	96.5022	834	965	95	inconclusive
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	88.4308	818	965	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	88.4117	826	965	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	88.2529	797	965	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	88.1267	820	965	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	87.8454	817	965	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	87.8161	813	965	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 15:47:14,141] [INFO] DFAST Taxonomy check result was written to GCA_003488145.1_ASM348814v1_genomic.fna/tc_result.tsv
[2023-06-17 15:47:14,141] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:47:14,142] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:47:14,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference/checkm_data
[2023-06-17 15:47:14,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:47:14,189] [INFO] Task started: CheckM
[2023-06-17 15:47:14,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003488145.1_ASM348814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003488145.1_ASM348814v1_genomic.fna/checkm_input GCA_003488145.1_ASM348814v1_genomic.fna/checkm_result
[2023-06-17 15:47:45,020] [INFO] Task succeeded: CheckM
[2023-06-17 15:47:45,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:47:45,044] [INFO] ===== Completeness check finished =====
[2023-06-17 15:47:45,045] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:47:45,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003488145.1_ASM348814v1_genomic.fna/markers.fasta)
[2023-06-17 15:47:45,045] [INFO] Task started: Blastn
[2023-06-17 15:47:45,046] [INFO] Running command: blastn -query GCA_003488145.1_ASM348814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dad03df-20a4-4f12-84cf-e83ca5c2cece/dqc_reference/reference_markers_gtdb.fasta -out GCA_003488145.1_ASM348814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:47:46,644] [INFO] Task succeeded: Blastn
[2023-06-17 15:47:46,650] [INFO] Selected 10 target genomes.
[2023-06-17 15:47:46,650] [INFO] Target genome list was writen to GCA_003488145.1_ASM348814v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:47:46,655] [INFO] Task started: fastANI
[2023-06-17 15:47:46,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf1bb218-29d2-4db8-9602-8c6ba6d7fdc5/GCA_003488145.1_ASM348814v1_genomic.fna.gz --refList GCA_003488145.1_ASM348814v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003488145.1_ASM348814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:47:55,202] [INFO] Task succeeded: fastANI
[2023-06-17 15:47:55,212] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:47:55,212] [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
GCA_003488145.1	s__Pseudomonas_A sp003488145	100.0	951	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.7169	97.61	97.61	0.74	0.74	2	conclusive
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	96.7169	882	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	96.6786	864	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	96.6441	845	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_900114065.1	s__Pseudomonas_A kunmingensis	96.6187	855	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.31	97.18	0.87	0.86	3	-
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	96.5378	859	965	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_014764705.1	s__Pseudomonas_A sp002692525	96.5014	836	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	96.4768	836	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	96.3216	804	965	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_000341615.1	s__Pseudomonas_A stutzeri_G	92.8512	821	965	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-17 15:47:55,214] [INFO] GTDB search result was written to GCA_003488145.1_ASM348814v1_genomic.fna/result_gtdb.tsv
[2023-06-17 15:47:55,215] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:47:55,218] [INFO] DFAST_QC result json was written to GCA_003488145.1_ASM348814v1_genomic.fna/dqc_result.json
[2023-06-17 15:47:55,219] [INFO] DFAST_QC completed!
[2023-06-17 15:47:55,219] [INFO] Total running time: 0h1m1s