[2023-06-18 10:25:57,320] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:25:57,324] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:25:57,324] [INFO] DQC Reference Directory: /var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference
[2023-06-18 10:25:59,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:25:59,324] [INFO] Task started: Prodigal
[2023-06-18 10:25:59,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg159b36cb-dfaf-4590-aa32-9e023ab75be5/GCA_018900115.1_ASM1890011v1_genomic.fna.gz | prodigal -d GCA_018900115.1_ASM1890011v1_genomic.fna/cds.fna -a GCA_018900115.1_ASM1890011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:26:07,689] [INFO] Task succeeded: Prodigal
[2023-06-18 10:26:07,690] [INFO] Task started: HMMsearch
[2023-06-18 10:26:07,690] [INFO] Running command: hmmsearch --tblout GCA_018900115.1_ASM1890011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference/reference_markers.hmm GCA_018900115.1_ASM1890011v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:26:07,916] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:26:07,918] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg159b36cb-dfaf-4590-aa32-9e023ab75be5/GCA_018900115.1_ASM1890011v1_genomic.fna.gz]
[2023-06-18 10:26:07,947] [INFO] Query marker FASTA was written to GCA_018900115.1_ASM1890011v1_genomic.fna/markers.fasta
[2023-06-18 10:26:07,947] [INFO] Task started: Blastn
[2023-06-18 10:26:07,948] [INFO] Running command: blastn -query GCA_018900115.1_ASM1890011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference/reference_markers.fasta -out GCA_018900115.1_ASM1890011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:08,697] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:08,702] [INFO] Selected 16 target genomes.
[2023-06-18 10:26:08,702] [INFO] Target genome list was writen to GCA_018900115.1_ASM1890011v1_genomic.fna/target_genomes.txt
[2023-06-18 10:26:08,704] [INFO] Task started: fastANI
[2023-06-18 10:26:08,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg159b36cb-dfaf-4590-aa32-9e023ab75be5/GCA_018900115.1_ASM1890011v1_genomic.fna.gz --refList GCA_018900115.1_ASM1890011v1_genomic.fna/target_genomes.txt --output GCA_018900115.1_ASM1890011v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:26:19,674] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:19,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:26:19,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:26:19,692] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:26:19,692] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 10:26:19,693] [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
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	84.3791	526	784	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.5819	252	784	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	78.4995	266	784	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	78.4838	271	784	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	78.2762	262	784	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	78.2516	257	784	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.9993	236	784	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	77.9361	215	784	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.9056	193	784	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	77.8415	170	784	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	77.7618	170	784	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.4878	194	784	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	77.3631	224	784	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.3172	211	784	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	77.3053	221	784	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.2533	188	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:26:19,697] [INFO] DFAST Taxonomy check result was written to GCA_018900115.1_ASM1890011v1_genomic.fna/tc_result.tsv
[2023-06-18 10:26:19,699] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:26:19,699] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:26:19,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference/checkm_data
[2023-06-18 10:26:19,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:26:19,734] [INFO] Task started: CheckM
[2023-06-18 10:26:19,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018900115.1_ASM1890011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018900115.1_ASM1890011v1_genomic.fna/checkm_input GCA_018900115.1_ASM1890011v1_genomic.fna/checkm_result
[2023-06-18 10:26:48,896] [INFO] Task succeeded: CheckM
[2023-06-18 10:26:48,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:26:48,923] [INFO] ===== Completeness check finished =====
[2023-06-18 10:26:48,924] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:26:48,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018900115.1_ASM1890011v1_genomic.fna/markers.fasta)
[2023-06-18 10:26:48,924] [INFO] Task started: Blastn
[2023-06-18 10:26:48,924] [INFO] Running command: blastn -query GCA_018900115.1_ASM1890011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc75d2173-2f7a-43ab-aa4f-dceef590403a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018900115.1_ASM1890011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:26:50,259] [INFO] Task succeeded: Blastn
[2023-06-18 10:26:50,267] [INFO] Selected 13 target genomes.
[2023-06-18 10:26:50,267] [INFO] Target genome list was writen to GCA_018900115.1_ASM1890011v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:26:50,272] [INFO] Task started: fastANI
[2023-06-18 10:26:50,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg159b36cb-dfaf-4590-aa32-9e023ab75be5/GCA_018900115.1_ASM1890011v1_genomic.fna.gz --refList GCA_018900115.1_ASM1890011v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018900115.1_ASM1890011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:26:59,322] [INFO] Task succeeded: fastANI
[2023-06-18 10:26:59,336] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:26:59,337] [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_013791765.1	s__Rhodoferax sp013791765	99.9229	749	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.97	99.92	0.98	0.96	7	conclusive
GCA_010365055.1	s__Rhodoferax sp010365055	87.3001	564	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013605.1	s__Rhodoferax ferrireducens	84.3732	527	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	95.18	95.18	0.88	0.88	2	-
GCA_017880985.1	s__Rhodoferax sp017880985	80.008	227	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927445.1	s__Rhodoferax sp012927445	79.7326	362	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.76	98.76	0.94	0.94	2	-
GCA_014859475.1	s__Rhodoferax sp014859475	79.3741	274	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828665.1	s__Rhodoferax sp903828665	79.2822	303	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.74	99.58	0.91	0.86	28	-
GCA_903920695.1	s__Rhodoferax sp903920695	78.976	307	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903876735.1	s__Rhodoferax sp903876735	78.9041	313	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.69	99.51	0.95	0.90	9	-
GCA_903914175.1	s__Rhodoferax sp903914175	78.838	283	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.22	98.03	0.89	0.84	13	-
GCF_001938565.1	s__Rhodoferax antarcticus	78.257	256	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.95	0.95	2	-
GCA_016185015.1	s__Hylemonella sp016185015	78.0944	237	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876045.1	s__Rhodoferax sp903876045	77.4885	154	784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.28	99.14	0.84	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-18 10:26:59,339] [INFO] GTDB search result was written to GCA_018900115.1_ASM1890011v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:26:59,339] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:26:59,343] [INFO] DFAST_QC result json was written to GCA_018900115.1_ASM1890011v1_genomic.fna/dqc_result.json
[2023-06-18 10:26:59,344] [INFO] DFAST_QC completed!
[2023-06-18 10:26:59,344] [INFO] Total running time: 0h1m2s