[2024-01-24 12:06:10,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference
[2024-01-24 12:06:13,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,064] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c272c9e-a2c4-406c-962a-0ffa798ddb7d/GCF_002355415.1_ASM235541v1_genomic.fna.gz | prodigal -d GCF_002355415.1_ASM235541v1_genomic.fna/cds.fna -a GCF_002355415.1_ASM235541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:24,522] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:24,522] [INFO] Task started: HMMsearch
[2024-01-24 12:06:24,523] [INFO] Running command: hmmsearch --tblout GCF_002355415.1_ASM235541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference/reference_markers.hmm GCF_002355415.1_ASM235541v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:24,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:24,863] [INFO] Found 6/6 markers.
[2024-01-24 12:06:24,908] [INFO] Query marker FASTA was written to GCF_002355415.1_ASM235541v1_genomic.fna/markers.fasta
[2024-01-24 12:06:24,909] [INFO] Task started: Blastn
[2024-01-24 12:06:24,909] [INFO] Running command: blastn -query GCF_002355415.1_ASM235541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference/reference_markers.fasta -out GCF_002355415.1_ASM235541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:25,909] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:25,913] [INFO] Selected 24 target genomes.
[2024-01-24 12:06:25,913] [INFO] Target genome list was writen to GCF_002355415.1_ASM235541v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:25,922] [INFO] Task started: fastANI
[2024-01-24 12:06:25,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c272c9e-a2c4-406c-962a-0ffa798ddb7d/GCF_002355415.1_ASM235541v1_genomic.fna.gz --refList GCF_002355415.1_ASM235541v1_genomic.fna/target_genomes.txt --output GCF_002355415.1_ASM235541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:46,073] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:46,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:46,074] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:46,093] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:46,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:46,093] [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
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	100.0	1319	1319	95	conclusive
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	78.4829	270	1319	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.258	179	1319	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.2256	139	1319	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	77.1478	187	1319	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.0757	133	1319	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.9658	124	1319	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.912	123	1319	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.6483	107	1319	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.4832	121	1319	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.458	252	1319	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.3843	151	1319	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.3581	105	1319	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.3571	188	1319	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.196	58	1319	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.0662	114	1319	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0419	142	1319	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.9571	174	1319	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	75.9123	184	1319	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.8955	107	1319	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	75.8682	205	1319	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	75.8602	207	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:46,095] [INFO] DFAST Taxonomy check result was written to GCF_002355415.1_ASM235541v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:46,096] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:46,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:46,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference/checkm_data
[2024-01-24 12:06:46,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:46,140] [INFO] Task started: CheckM
[2024-01-24 12:06:46,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355415.1_ASM235541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355415.1_ASM235541v1_genomic.fna/checkm_input GCF_002355415.1_ASM235541v1_genomic.fna/checkm_result
[2024-01-24 12:07:23,765] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:23,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:23,788] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:23,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:23,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355415.1_ASM235541v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:23,789] [INFO] Task started: Blastn
[2024-01-24 12:07:23,789] [INFO] Running command: blastn -query GCF_002355415.1_ASM235541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7454352-9d90-4cbf-8c07-c88b9f807d8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355415.1_ASM235541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:25,732] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:25,735] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:25,735] [INFO] Target genome list was writen to GCF_002355415.1_ASM235541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:25,751] [INFO] Task started: fastANI
[2024-01-24 12:07:25,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c272c9e-a2c4-406c-962a-0ffa798ddb7d/GCF_002355415.1_ASM235541v1_genomic.fna.gz --refList GCF_002355415.1_ASM235541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355415.1_ASM235541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:35,942] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,960] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:35,960] [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_002355415.1	s__Sulfurifustis variabilis	100.0	1319	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfurifustis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004298065.1	s__SCRL01 sp004298065	78.6099	310	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__SCRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001785175.1	s__MFSY01 sp001785175	78.6061	225	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__MFSY01	95.0	97.98	97.98	0.76	0.76	2	-
GCF_002355735.1	s__Sulfuricaulis limicola	78.4975	269	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001785115.1	s__RBG-16-65-34 sp001785115	78.3079	240	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__RBG-16-65-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200465.1	s__Sulfuricaulis sp016200465	78.233	201	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	77.1185	189	1319	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	-
GCA_016199745.1	s__JACQFZ01 sp016199745	76.7729	173	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__JACQFZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	76.305	217	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCF_004366735.1	s__Thiohalophilus thiocyanatoxydans	76.2039	59	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__Thiohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	76.1341	107	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054615.1	s__FEN-1219 sp011054615	76.1211	163	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__FEN-1219	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	76.0052	187	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCA_002256785.1	s__Thiobacillus sp002256785	76.003	64	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	75.9569	174	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_004340905.1	s__Rubrivivax gelatinosus	75.84	210	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,962] [INFO] GTDB search result was written to GCF_002355415.1_ASM235541v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:35,963] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:35,969] [INFO] DFAST_QC result json was written to GCF_002355415.1_ASM235541v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:35,970] [INFO] DFAST_QC completed!
[2024-01-24 12:07:35,970] [INFO] Total running time: 0h1m26s