[2024-01-24 12:37:24,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference
[2024-01-24 12:37:25,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:25,941] [INFO] Task started: Prodigal
[2024-01-24 12:37:25,941] [INFO] Running command: gunzip -c /var/lib/cwl/stge36997b1-d163-4bad-80cd-7fd987750281/GCF_009882935.1_ASM988293v1_genomic.fna.gz | prodigal -d GCF_009882935.1_ASM988293v1_genomic.fna/cds.fna -a GCF_009882935.1_ASM988293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:36,664] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:36,665] [INFO] Task started: HMMsearch
[2024-01-24 12:37:36,665] [INFO] Running command: hmmsearch --tblout GCF_009882935.1_ASM988293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference/reference_markers.hmm GCF_009882935.1_ASM988293v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:36,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:36,942] [INFO] Found 6/6 markers.
[2024-01-24 12:37:36,980] [INFO] Query marker FASTA was written to GCF_009882935.1_ASM988293v1_genomic.fna/markers.fasta
[2024-01-24 12:37:36,981] [INFO] Task started: Blastn
[2024-01-24 12:37:36,981] [INFO] Running command: blastn -query GCF_009882935.1_ASM988293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference/reference_markers.fasta -out GCF_009882935.1_ASM988293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:37,798] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:37,802] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:37,802] [INFO] Target genome list was writen to GCF_009882935.1_ASM988293v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:37,808] [INFO] Task started: fastANI
[2024-01-24 12:37:37,808] [INFO] Running command: fastANI --query /var/lib/cwl/stge36997b1-d163-4bad-80cd-7fd987750281/GCF_009882935.1_ASM988293v1_genomic.fna.gz --refList GCF_009882935.1_ASM988293v1_genomic.fna/target_genomes.txt --output GCF_009882935.1_ASM988293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:47,753] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:47,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:47,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:47,764] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:47,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:47,764] [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
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	100.0	1266	1266	95	conclusive
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	99.9771	1250	1266	95	conclusive
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	80.8986	666	1266	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	80.0903	586	1266	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	77.0455	222	1266	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.4926	111	1266	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.2335	100	1266	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1295	74	1266	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.0253	65	1266	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	75.8388	52	1266	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.8196	80	1266	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	75.7868	58	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:47,766] [INFO] DFAST Taxonomy check result was written to GCF_009882935.1_ASM988293v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:47,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:47,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:47,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference/checkm_data
[2024-01-24 12:37:47,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:47,806] [INFO] Task started: CheckM
[2024-01-24 12:37:47,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009882935.1_ASM988293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009882935.1_ASM988293v1_genomic.fna/checkm_input GCF_009882935.1_ASM988293v1_genomic.fna/checkm_result
[2024-01-24 12:38:22,958] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:22,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:22,986] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:22,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:22,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009882935.1_ASM988293v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:22,988] [INFO] Task started: Blastn
[2024-01-24 12:38:22,988] [INFO] Running command: blastn -query GCF_009882935.1_ASM988293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a601af9-c27a-4c91-8515-db6d51930e59/dqc_reference/reference_markers_gtdb.fasta -out GCF_009882935.1_ASM988293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:24,392] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:24,394] [INFO] Selected 8 target genomes.
[2024-01-24 12:38:24,394] [INFO] Target genome list was writen to GCF_009882935.1_ASM988293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:24,405] [INFO] Task started: fastANI
[2024-01-24 12:38:24,405] [INFO] Running command: fastANI --query /var/lib/cwl/stge36997b1-d163-4bad-80cd-7fd987750281/GCF_009882935.1_ASM988293v1_genomic.fna.gz --refList GCF_009882935.1_ASM988293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009882935.1_ASM988293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:30,996] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:31,014] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:31,014] [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_009882935.1	s__Sneathiella chungangensis	100.0	1266	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017313765.1	s__Sneathiella sp017313765	80.8986	666	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706985.1	s__Sneathiella sp002706985	80.533	563	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCF_009882915.1	s__Sneathiella litorea	80.0927	585	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694385.1	s__Sneathiella sp002694385	79.6937	559	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCA_006226265.1	s__Sneathiella sp006226265	78.8569	333	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	75.5906	104	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	75.5857	68	1266	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:31,016] [INFO] GTDB search result was written to GCF_009882935.1_ASM988293v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:31,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:31,021] [INFO] DFAST_QC result json was written to GCF_009882935.1_ASM988293v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:31,021] [INFO] DFAST_QC completed!
[2024-01-24 12:38:31,021] [INFO] Total running time: 0h1m6s