[2024-01-24 10:49:34,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference
[2024-01-24 10:49:35,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,685] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b8ea90e-7ec1-4e17-bfa6-2604a0fd0a96/GCF_003345655.1_ASM334565v1_genomic.fna.gz | prodigal -d GCF_003345655.1_ASM334565v1_genomic.fna/cds.fna -a GCF_003345655.1_ASM334565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:46,830] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:46,830] [INFO] Task started: HMMsearch
[2024-01-24 10:49:46,831] [INFO] Running command: hmmsearch --tblout GCF_003345655.1_ASM334565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference/reference_markers.hmm GCF_003345655.1_ASM334565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:47,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:47,139] [INFO] Found 6/6 markers.
[2024-01-24 10:49:47,195] [INFO] Query marker FASTA was written to GCF_003345655.1_ASM334565v1_genomic.fna/markers.fasta
[2024-01-24 10:49:47,196] [INFO] Task started: Blastn
[2024-01-24 10:49:47,196] [INFO] Running command: blastn -query GCF_003345655.1_ASM334565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference/reference_markers.fasta -out GCF_003345655.1_ASM334565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:48,027] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:48,031] [INFO] Selected 22 target genomes.
[2024-01-24 10:49:48,031] [INFO] Target genome list was writen to GCF_003345655.1_ASM334565v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:48,040] [INFO] Task started: fastANI
[2024-01-24 10:49:48,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8ea90e-7ec1-4e17-bfa6-2604a0fd0a96/GCF_003345655.1_ASM334565v1_genomic.fna.gz --refList GCF_003345655.1_ASM334565v1_genomic.fna/target_genomes.txt --output GCF_003345655.1_ASM334565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:03,701] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:03,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:03,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:03,721] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:50:03,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:03,722] [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
Motiliproteus coralliicola	strain=C34	GCA_003345655.1	2283196	2283196	type	True	100.0	1387	1389	95	conclusive
Motiliproteus sediminis	strain=HS6	GCA_017912535.1	1468178	1468178	type	True	78.2081	291	1389	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.9958	310	1389	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	77.6516	215	1389	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	77.584	217	1389	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	77.5028	214	1389	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.4926	187	1389	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.4242	183	1389	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.1469	135	1389	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	77.065	195	1389	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	77.0552	129	1389	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.9612	121	1389	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.7592	129	1389	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.7257	144	1389	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6537	168	1389	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	76.6069	106	1389	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.4981	135	1389	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.4824	132	1389	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.436	132	1389	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	76.3566	89	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:03,724] [INFO] DFAST Taxonomy check result was written to GCF_003345655.1_ASM334565v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:03,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:03,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:03,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference/checkm_data
[2024-01-24 10:50:03,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:03,769] [INFO] Task started: CheckM
[2024-01-24 10:50:03,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003345655.1_ASM334565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003345655.1_ASM334565v1_genomic.fna/checkm_input GCF_003345655.1_ASM334565v1_genomic.fna/checkm_result
[2024-01-24 10:50:41,452] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:41,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:41,480] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:41,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:41,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003345655.1_ASM334565v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:41,481] [INFO] Task started: Blastn
[2024-01-24 10:50:41,481] [INFO] Running command: blastn -query GCF_003345655.1_ASM334565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31eeecba-f520-479a-a1d7-4ea5017255fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003345655.1_ASM334565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:43,000] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:43,005] [INFO] Selected 17 target genomes.
[2024-01-24 10:50:43,005] [INFO] Target genome list was writen to GCF_003345655.1_ASM334565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:43,019] [INFO] Task started: fastANI
[2024-01-24 10:50:43,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8ea90e-7ec1-4e17-bfa6-2604a0fd0a96/GCF_003345655.1_ASM334565v1_genomic.fna.gz --refList GCF_003345655.1_ASM334565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003345655.1_ASM334565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:56,123] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:56,141] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:56,141] [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_003345655.1	s__Motiliproteus coralliicola	100.0	1386	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017912535.1	s__Motiliproteus sediminis	78.2081	291	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309075.1	s__Motiliproteus sp017309075	77.9263	304	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195305.1	s__Motiliproteus sp004195305	77.7615	224	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	77.649	216	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	77.5941	217	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	77.495	191	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.4027	184	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	77.0821	166	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	77.0668	198	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001968815.1	s__Motiliproteus sp001968815	76.9693	82	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	76.7593	131	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756775.1	s__Pseudomonas_A saudiphocaensis	76.567	108	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.10	98.10	0.92	0.90	3	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.5595	153	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	76.3609	90	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	76.3246	143	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402545.1	s__Saccharospirillum sp018402545	76.1903	50	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:56,143] [INFO] GTDB search result was written to GCF_003345655.1_ASM334565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:56,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:56,148] [INFO] DFAST_QC result json was written to GCF_003345655.1_ASM334565v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:56,148] [INFO] DFAST_QC completed!
[2024-01-24 10:50:56,149] [INFO] Total running time: 0h1m22s