[2024-01-24 13:57:40,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:40,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:40,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference
[2024-01-24 13:57:41,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:41,542] [INFO] Task started: Prodigal
[2024-01-24 13:57:41,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a8f4a52-bb89-44e6-9220-0d907d11cc33/GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/cds.fna -a GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:53,608] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:53,608] [INFO] Task started: HMMsearch
[2024-01-24 13:57:53,609] [INFO] Running command: hmmsearch --tblout GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference/reference_markers.hmm GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:53,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:53,846] [INFO] Found 6/6 markers.
[2024-01-24 13:57:53,883] [INFO] Query marker FASTA was written to GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:53,883] [INFO] Task started: Blastn
[2024-01-24 13:57:53,884] [INFO] Running command: blastn -query GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference/reference_markers.fasta -out GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:54,829] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:54,833] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:54,833] [INFO] Target genome list was writen to GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:54,841] [INFO] Task started: fastANI
[2024-01-24 13:57:54,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a8f4a52-bb89-44e6-9220-0d907d11cc33/GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna.gz --refList GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:09,594] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:09,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:09,610] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:09,610] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:09,610] [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
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	100.0	1290	1295	95	conclusive
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	99.9795	1265	1295	95	conclusive
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	85.0963	802	1295	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	84.4552	774	1295	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	84.3746	777	1295	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	84.2212	776	1295	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	84.1995	770	1295	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	84.1239	713	1295	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	83.8108	744	1295	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	83.7572	762	1295	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	82.8618	693	1295	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	82.8581	666	1295	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	82.7892	711	1295	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.0728	509	1295	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	80.048	603	1295	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.9037	484	1295	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.6864	545	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,613] [INFO] DFAST Taxonomy check result was written to GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:09,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:09,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:09,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference/checkm_data
[2024-01-24 13:58:09,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:09,656] [INFO] Task started: CheckM
[2024-01-24 13:58:09,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/checkm_input GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:58:47,851] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:47,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,871] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:47,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:47,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:58:47,872] [INFO] Task started: Blastn
[2024-01-24 13:58:47,872] [INFO] Running command: blastn -query GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc266dfd5-a818-432e-96d6-2e78bcd8add6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,804] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,808] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:49,808] [INFO] Target genome list was writen to GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:49,823] [INFO] Task started: fastANI
[2024-01-24 13:58:49,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a8f4a52-bb89-44e6-9220-0d907d11cc33/GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna.gz --refList GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:01,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:01,808] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:01,808] [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_000763905.1	s__Paracoccus halophilus	99.9795	1265	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003337565.1	s__Paracoccus lutimaris	85.0831	803	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	84.4295	779	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000518925.1	s__Paracoccus sp000518925	84.4064	796	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCA_018056045.1	s__Paracoccus sp018056045	84.2514	525	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763885.1	s__Paracoccus versutus	84.2503	774	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_016446475.1	s__Paracoccus binzhouensis	84.2427	767	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	84.2393	804	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156255.1	s__Paracoccus thiocyanatus	84.1558	709	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_001546115.1	s__Paracoccus aminovorans_B	83.8058	787	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_900005615.1	s__Paracoccus aminovorans	83.7891	758	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009711185.1	s__Paracoccus limosus	83.0853	710	1295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:01,811] [INFO] GTDB search result was written to GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:01,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:01,816] [INFO] DFAST_QC result json was written to GCF_900111785.1_IMG-taxon_2617270913_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:01,817] [INFO] DFAST_QC completed!
[2024-01-24 13:59:01,817] [INFO] Total running time: 0h1m21s