[2024-01-24 12:06:23,981] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference
[2024-01-24 12:06:25,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,302] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg28b8bf41-021f-4d83-93b9-7bf72ff19636/GCF_003337735.1_ASM333773v1_genomic.fna.gz | prodigal -d GCF_003337735.1_ASM333773v1_genomic.fna/cds.fna -a GCF_003337735.1_ASM333773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:37,929] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:37,930] [INFO] Task started: HMMsearch
[2024-01-24 12:06:37,930] [INFO] Running command: hmmsearch --tblout GCF_003337735.1_ASM333773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference/reference_markers.hmm GCF_003337735.1_ASM333773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:38,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:38,174] [INFO] Found 6/6 markers.
[2024-01-24 12:06:38,209] [INFO] Query marker FASTA was written to GCF_003337735.1_ASM333773v1_genomic.fna/markers.fasta
[2024-01-24 12:06:38,210] [INFO] Task started: Blastn
[2024-01-24 12:06:38,210] [INFO] Running command: blastn -query GCF_003337735.1_ASM333773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference/reference_markers.fasta -out GCF_003337735.1_ASM333773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:39,219] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:39,223] [INFO] Selected 26 target genomes.
[2024-01-24 12:06:39,223] [INFO] Target genome list was writen to GCF_003337735.1_ASM333773v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:39,231] [INFO] Task started: fastANI
[2024-01-24 12:06:39,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b8bf41-021f-4d83-93b9-7bf72ff19636/GCF_003337735.1_ASM333773v1_genomic.fna.gz --refList GCF_003337735.1_ASM333773v1_genomic.fna/target_genomes.txt --output GCF_003337735.1_ASM333773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:59,098] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:59,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:59,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:59,118] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:59,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:59,119] [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
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	100.0	1371	1373	95	conclusive
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	78.773	362	1373	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	78.519	404	1373	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	78.0613	349	1373	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	78.0237	345	1373	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.7727	325	1373	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	77.7502	286	1373	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	77.7396	269	1373	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	77.5047	151	1373	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	77.4161	319	1373	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	77.3387	208	1373	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.3037	212	1373	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	77.2757	339	1373	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.1092	265	1373	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9499	304	1373	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.9159	246	1373	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.8508	267	1373	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.6476	204	1373	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	76.561	269	1373	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.56	250	1373	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.3066	213	1373	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	76.0093	98	1373	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	75.4171	168	1373	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	75.2204	127	1373	95	below_threshold
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	74.995	180	1373	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	74.935	142	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,121] [INFO] DFAST Taxonomy check result was written to GCF_003337735.1_ASM333773v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:59,122] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:59,122] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:59,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference/checkm_data
[2024-01-24 12:06:59,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:59,164] [INFO] Task started: CheckM
[2024-01-24 12:06:59,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337735.1_ASM333773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337735.1_ASM333773v1_genomic.fna/checkm_input GCF_003337735.1_ASM333773v1_genomic.fna/checkm_result
[2024-01-24 12:07:37,483] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:37,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:37,499] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:37,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:37,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337735.1_ASM333773v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:37,500] [INFO] Task started: Blastn
[2024-01-24 12:07:37,500] [INFO] Running command: blastn -query GCF_003337735.1_ASM333773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbecc2a-2787-4e55-9b3b-99c94e931a4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337735.1_ASM333773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:39,193] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:39,199] [INFO] Selected 25 target genomes.
[2024-01-24 12:07:39,199] [INFO] Target genome list was writen to GCF_003337735.1_ASM333773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:39,237] [INFO] Task started: fastANI
[2024-01-24 12:07:39,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b8bf41-021f-4d83-93b9-7bf72ff19636/GCF_003337735.1_ASM333773v1_genomic.fna.gz --refList GCF_003337735.1_ASM333773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337735.1_ASM333773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:56,394] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:56,413] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:56,413] [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_003337735.1	s__Thioalbus denitrificans	100.0	1371	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	78.7729	362	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	78.7032	346	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	78.5121	385	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	78.4973	395	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	78.4945	407	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	78.3312	281	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	78.3131	331	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	78.2897	343	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_011371455.1	s__DRQN01 sp011371455	78.211	198	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_015491615.1	s__S140-43 sp015491615	78.1311	191	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S140-43	95.0	99.42	99.32	0.88	0.87	3	-
GCA_002699185.1	s__Thiohalobacter sp002699185	78.1181	276	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	78.0427	351	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	78.0254	345	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	78.0187	288	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348725.1	s__GCA-013348725 sp013348725	77.909	281	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376325.1	s__Sulfurivermis sp002376325	77.843	238	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	77.8217	268	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225005.1	s__Ectothiorhodospira sp000225005	77.7338	208	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	77.6911	321	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCA_011389995.1	s__JAABTG01 sp011389995	77.5671	293	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAABTG01;f__JAABTG01;g__JAABTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906305.1	s__Alcanivorax marinus_B	76.8879	264	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702725.1	s__BRH-c0 sp002702725	76.6053	53	1373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	75.1082	261	1373	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	75.0226	252	1373	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,415] [INFO] GTDB search result was written to GCF_003337735.1_ASM333773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:56,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:56,420] [INFO] DFAST_QC result json was written to GCF_003337735.1_ASM333773v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:56,420] [INFO] DFAST_QC completed!
[2024-01-24 12:07:56,420] [INFO] Total running time: 0h1m32s