[2024-01-24 13:50:10,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference
[2024-01-24 13:50:12,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:12,044] [INFO] Task started: Prodigal
[2024-01-24 13:50:12,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg88302176-3f5b-4ab0-9912-cca0a776040a/GCF_012720115.1_ASM1272011v1_genomic.fna.gz | prodigal -d GCF_012720115.1_ASM1272011v1_genomic.fna/cds.fna -a GCF_012720115.1_ASM1272011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:23,515] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:23,516] [INFO] Task started: HMMsearch
[2024-01-24 13:50:23,516] [INFO] Running command: hmmsearch --tblout GCF_012720115.1_ASM1272011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference/reference_markers.hmm GCF_012720115.1_ASM1272011v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:23,780] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:23,781] [INFO] Found 6/6 markers.
[2024-01-24 13:50:23,811] [INFO] Query marker FASTA was written to GCF_012720115.1_ASM1272011v1_genomic.fna/markers.fasta
[2024-01-24 13:50:23,811] [INFO] Task started: Blastn
[2024-01-24 13:50:23,811] [INFO] Running command: blastn -query GCF_012720115.1_ASM1272011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference/reference_markers.fasta -out GCF_012720115.1_ASM1272011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:24,571] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:24,574] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:24,574] [INFO] Target genome list was writen to GCF_012720115.1_ASM1272011v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:24,583] [INFO] Task started: fastANI
[2024-01-24 13:50:24,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg88302176-3f5b-4ab0-9912-cca0a776040a/GCF_012720115.1_ASM1272011v1_genomic.fna.gz --refList GCF_012720115.1_ASM1272011v1_genomic.fna/target_genomes.txt --output GCF_012720115.1_ASM1272011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:38,087] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:38,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:38,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:38,099] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:38,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:38,099] [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 chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	100.0	1174	1174	95	conclusive
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	77.0119	194	1174	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	76.8848	229	1174	95	below_threshold
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	76.8561	152	1174	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	76.8498	232	1174	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	76.7749	156	1174	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	76.6928	174	1174	95	below_threshold
Thalassospira marina	strain=CSC3H3	GCA_002844375.1	2048283	2048283	type	True	76.1136	67	1174	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	75.6715	56	1174	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	75.6715	56	1174	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	75.5551	50	1174	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.3403	67	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,101] [INFO] DFAST Taxonomy check result was written to GCF_012720115.1_ASM1272011v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:38,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:38,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:38,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference/checkm_data
[2024-01-24 13:50:38,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:38,137] [INFO] Task started: CheckM
[2024-01-24 13:50:38,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012720115.1_ASM1272011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012720115.1_ASM1272011v1_genomic.fna/checkm_input GCF_012720115.1_ASM1272011v1_genomic.fna/checkm_result
[2024-01-24 13:51:13,887] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:13,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,907] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:13,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:13,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012720115.1_ASM1272011v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:13,908] [INFO] Task started: Blastn
[2024-01-24 13:51:13,908] [INFO] Running command: blastn -query GCF_012720115.1_ASM1272011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c10ffa-b0aa-46eb-9bed-db5b998742ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_012720115.1_ASM1272011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:15,223] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:15,227] [INFO] Selected 21 target genomes.
[2024-01-24 13:51:15,227] [INFO] Target genome list was writen to GCF_012720115.1_ASM1272011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:15,261] [INFO] Task started: fastANI
[2024-01-24 13:51:15,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg88302176-3f5b-4ab0-9912-cca0a776040a/GCF_012720115.1_ASM1272011v1_genomic.fna.gz --refList GCF_012720115.1_ASM1272011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012720115.1_ASM1272011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:27,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:27,912] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:27,912] [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_012720115.1	s__Sneathiella chinensis	100.0	1174	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428885.1	s__Sneathiella sp002428885	77.2634	245	1174	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	77.0853	232	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCF_017313765.1	s__Sneathiella sp017313765	77.0119	194	1174	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	76.9945	164	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCA_006226265.1	s__Sneathiella sp006226265	76.9819	141	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882935.1	s__Sneathiella chungangensis	76.8848	229	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012932565.1	s__Sneathiella limimaris	76.8703	151	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015143595.1	s__Sneathiella sp015143595	76.8546	164	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882915.1	s__Sneathiella litorea	76.7886	154	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720095.1	s__Sneathiella aquimaris	76.6928	174	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844375.1	s__Thalassospira marina	76.1136	67	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.72	97.72	0.93	0.93	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.8805	81	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	75.8003	50	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796975.1	s__Ferrovibrio sp002796975	75.7714	59	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	75.6715	56	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004522155.1	s__Paracoccus luteus	75.5551	50	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:27,914] [INFO] GTDB search result was written to GCF_012720115.1_ASM1272011v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:27,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:27,918] [INFO] DFAST_QC result json was written to GCF_012720115.1_ASM1272011v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:27,918] [INFO] DFAST_QC completed!
[2024-01-24 13:51:27,918] [INFO] Total running time: 0h1m17s