[2024-01-24 13:27:58,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference
[2024-01-24 13:28:00,107] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:00,108] [INFO] Task started: Prodigal
[2024-01-24 13:28:00,108] [INFO] Running command: gunzip -c /var/lib/cwl/stga8ed2066-4733-40e6-88e1-91b8f94027d3/GCF_008086175.1_ASM808617v1_genomic.fna.gz | prodigal -d GCF_008086175.1_ASM808617v1_genomic.fna/cds.fna -a GCF_008086175.1_ASM808617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:09,877] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:09,877] [INFO] Task started: HMMsearch
[2024-01-24 13:28:09,877] [INFO] Running command: hmmsearch --tblout GCF_008086175.1_ASM808617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference/reference_markers.hmm GCF_008086175.1_ASM808617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:10,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:10,155] [INFO] Found 6/6 markers.
[2024-01-24 13:28:10,188] [INFO] Query marker FASTA was written to GCF_008086175.1_ASM808617v1_genomic.fna/markers.fasta
[2024-01-24 13:28:10,189] [INFO] Task started: Blastn
[2024-01-24 13:28:10,189] [INFO] Running command: blastn -query GCF_008086175.1_ASM808617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference/reference_markers.fasta -out GCF_008086175.1_ASM808617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:10,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:10,885] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:10,886] [INFO] Target genome list was writen to GCF_008086175.1_ASM808617v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:10,900] [INFO] Task started: fastANI
[2024-01-24 13:28:10,900] [INFO] Running command: fastANI --query /var/lib/cwl/stga8ed2066-4733-40e6-88e1-91b8f94027d3/GCF_008086175.1_ASM808617v1_genomic.fna.gz --refList GCF_008086175.1_ASM808617v1_genomic.fna/target_genomes.txt --output GCF_008086175.1_ASM808617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:22,872] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:22,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:22,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:22,889] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:22,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:22,889] [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
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	81.7002	658	1065	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	78.0725	313	1065	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	78.0351	354	1065	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	77.8257	263	1065	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.8256	364	1065	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.76	240	1065	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.7202	240	1065	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.7202	240	1065	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	77.6631	226	1065	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	77.6396	235	1065	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.6121	253	1065	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.5203	172	1065	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	77.4925	248	1065	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	77.4853	255	1065	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.3722	178	1065	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.3619	165	1065	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	77.3531	263	1065	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.7133	115	1065	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.6382	101	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:22,891] [INFO] DFAST Taxonomy check result was written to GCF_008086175.1_ASM808617v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:22,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:22,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:22,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference/checkm_data
[2024-01-24 13:28:22,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:22,929] [INFO] Task started: CheckM
[2024-01-24 13:28:22,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008086175.1_ASM808617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008086175.1_ASM808617v1_genomic.fna/checkm_input GCF_008086175.1_ASM808617v1_genomic.fna/checkm_result
[2024-01-24 13:28:57,396] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:57,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,415] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:57,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:57,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008086175.1_ASM808617v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:57,416] [INFO] Task started: Blastn
[2024-01-24 13:28:57,416] [INFO] Running command: blastn -query GCF_008086175.1_ASM808617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb6aaff-9bf1-412a-b980-c2fe3891cb6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008086175.1_ASM808617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:58,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:58,345] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:58,345] [INFO] Target genome list was writen to GCF_008086175.1_ASM808617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:58,375] [INFO] Task started: fastANI
[2024-01-24 13:28:58,375] [INFO] Running command: fastANI --query /var/lib/cwl/stga8ed2066-4733-40e6-88e1-91b8f94027d3/GCF_008086175.1_ASM808617v1_genomic.fna.gz --refList GCF_008086175.1_ASM808617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008086175.1_ASM808617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:07,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:07,538] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:07,538] [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_008086175.1	s__Bizionia saleffrena	100.0	1064	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	99.23	99.23	0.93	0.93	2	conclusive
GCA_018067115.1	s__Bizionia sp018067115	84.8575	558	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107625.1	s__Bizionia paragorgiae	81.7106	657	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Bizionia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	78.3491	323	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_002831665.1	s__Lacinutrix sp002831665	78.213	344	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	78.0797	313	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	78.0363	355	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	77.9909	296	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.9648	324	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000211855.2	s__Lacinutrix sp000211855	77.8256	330	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.8253	364	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	77.8215	264	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_008806375.1	s__Tamlana_A haliotis	77.5259	173	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.3532	262	1065	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:07,540] [INFO] GTDB search result was written to GCF_008086175.1_ASM808617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:07,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:07,545] [INFO] DFAST_QC result json was written to GCF_008086175.1_ASM808617v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:07,546] [INFO] DFAST_QC completed!
[2024-01-24 13:29:07,546] [INFO] Total running time: 0h1m9s