[2023-06-27 14:44:03,943] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:44:03,945] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:44:03,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference
[2023-06-27 14:44:05,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:44:05,182] [INFO] Task started: Prodigal
[2023-06-27 14:44:05,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg575f3eca-9468-4c74-b372-0ffc7cab9d5f/GCA_002430985.1_ASM243098v1_genomic.fna.gz | prodigal -d GCA_002430985.1_ASM243098v1_genomic.fna/cds.fna -a GCA_002430985.1_ASM243098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:44:14,465] [INFO] Task succeeded: Prodigal
[2023-06-27 14:44:14,466] [INFO] Task started: HMMsearch
[2023-06-27 14:44:14,466] [INFO] Running command: hmmsearch --tblout GCA_002430985.1_ASM243098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference/reference_markers.hmm GCA_002430985.1_ASM243098v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:44:14,723] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:44:14,725] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg575f3eca-9468-4c74-b372-0ffc7cab9d5f/GCA_002430985.1_ASM243098v1_genomic.fna.gz]
[2023-06-27 14:44:14,764] [INFO] Query marker FASTA was written to GCA_002430985.1_ASM243098v1_genomic.fna/markers.fasta
[2023-06-27 14:44:14,764] [INFO] Task started: Blastn
[2023-06-27 14:44:14,764] [INFO] Running command: blastn -query GCA_002430985.1_ASM243098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference/reference_markers.fasta -out GCA_002430985.1_ASM243098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:15,530] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:15,535] [INFO] Selected 9 target genomes.
[2023-06-27 14:44:15,535] [INFO] Target genome list was writen to GCA_002430985.1_ASM243098v1_genomic.fna/target_genomes.txt
[2023-06-27 14:44:15,537] [INFO] Task started: fastANI
[2023-06-27 14:44:15,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg575f3eca-9468-4c74-b372-0ffc7cab9d5f/GCA_002430985.1_ASM243098v1_genomic.fna.gz --refList GCA_002430985.1_ASM243098v1_genomic.fna/target_genomes.txt --output GCA_002430985.1_ASM243098v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:44:23,901] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:23,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:44:23,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:44:23,912] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-27 14:44:23,912] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-27 14:44:23,912] [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_024397575.1	1211807	1211807	type	True	97.0722	967	1048	95	inconclusive
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	97.0139	979	1048	95	inconclusive
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	96.8582	947	1048	95	inconclusive
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	89.0441	912	1048	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	89.0421	915	1048	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	88.5598	920	1048	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	88.534	926	1048	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	87.714	909	1048	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	87.6804	915	1048	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:44:23,915] [INFO] DFAST Taxonomy check result was written to GCA_002430985.1_ASM243098v1_genomic.fna/tc_result.tsv
[2023-06-27 14:44:23,916] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:44:23,916] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:44:23,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference/checkm_data
[2023-06-27 14:44:23,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:44:23,956] [INFO] Task started: CheckM
[2023-06-27 14:44:23,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002430985.1_ASM243098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002430985.1_ASM243098v1_genomic.fna/checkm_input GCA_002430985.1_ASM243098v1_genomic.fna/checkm_result
[2023-06-27 14:44:54,719] [INFO] Task succeeded: CheckM
[2023-06-27 14:44:54,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:44:54,748] [INFO] ===== Completeness check finished =====
[2023-06-27 14:44:54,748] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:44:54,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002430985.1_ASM243098v1_genomic.fna/markers.fasta)
[2023-06-27 14:44:54,749] [INFO] Task started: Blastn
[2023-06-27 14:44:54,749] [INFO] Running command: blastn -query GCA_002430985.1_ASM243098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0271dc78-8b44-45ba-b86b-cf467ed80108/dqc_reference/reference_markers_gtdb.fasta -out GCA_002430985.1_ASM243098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:56,074] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:56,080] [INFO] Selected 8 target genomes.
[2023-06-27 14:44:56,080] [INFO] Target genome list was writen to GCA_002430985.1_ASM243098v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:44:56,081] [INFO] Task started: fastANI
[2023-06-27 14:44:56,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg575f3eca-9468-4c74-b372-0ffc7cab9d5f/GCA_002430985.1_ASM243098v1_genomic.fna.gz --refList GCA_002430985.1_ASM243098v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002430985.1_ASM243098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:45:03,607] [INFO] Task succeeded: fastANI
[2023-06-27 14:45:03,619] [INFO] Found 8 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-27 14:45:03,620] [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_003935375.1	s__Pseudomonas_A xanthomarina_A	97.6174	973	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	inconclusive
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	97.2656	980	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	inconclusive
GCF_014764705.1	s__Pseudomonas_A sp002692525	97.1307	956	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	inconclusive
GCA_007713455.1	s__Pseudomonas_A sp007713455	97.0418	969	1048	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_900114065.1	s__Pseudomonas_A kunmingensis	97.0139	979	1048	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	97.0138	980	1048	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_000495915.1	s__Pseudomonas_A chloritidismutans	96.8582	947	1048	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	96.681	918	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-27 14:45:03,622] [INFO] GTDB search result was written to GCA_002430985.1_ASM243098v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:45:03,622] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:45:03,626] [INFO] DFAST_QC result json was written to GCA_002430985.1_ASM243098v1_genomic.fna/dqc_result.json
[2023-06-27 14:45:03,626] [INFO] DFAST_QC completed!
[2023-06-27 14:45:03,626] [INFO] Total running time: 0h0m60s