[2024-01-25 18:43:35,515] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference
[2024-01-25 18:43:36,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,652] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,653] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2b9b948-d048-4b1e-8a49-862cbae6c21e/GCF_001418085.1_ASM141808v1_genomic.fna.gz | prodigal -d GCF_001418085.1_ASM141808v1_genomic.fna/cds.fna -a GCF_001418085.1_ASM141808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:44,855] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:44,856] [INFO] Task started: HMMsearch
[2024-01-25 18:43:44,856] [INFO] Running command: hmmsearch --tblout GCF_001418085.1_ASM141808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference/reference_markers.hmm GCF_001418085.1_ASM141808v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:45,070] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:45,071] [INFO] Found 6/6 markers.
[2024-01-25 18:43:45,099] [INFO] Query marker FASTA was written to GCF_001418085.1_ASM141808v1_genomic.fna/markers.fasta
[2024-01-25 18:43:45,099] [INFO] Task started: Blastn
[2024-01-25 18:43:45,099] [INFO] Running command: blastn -query GCF_001418085.1_ASM141808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference/reference_markers.fasta -out GCF_001418085.1_ASM141808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:45,751] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:45,754] [INFO] Selected 17 target genomes.
[2024-01-25 18:43:45,754] [INFO] Target genome list was writen to GCF_001418085.1_ASM141808v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:45,760] [INFO] Task started: fastANI
[2024-01-25 18:43:45,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2b9b948-d048-4b1e-8a49-862cbae6c21e/GCF_001418085.1_ASM141808v1_genomic.fna.gz --refList GCF_001418085.1_ASM141808v1_genomic.fna/target_genomes.txt --output GCF_001418085.1_ASM141808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:58,269] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:58,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:58,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:58,280] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:58,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:58,281] [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
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	100.0	1193	1199	95	conclusive
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	87.3108	954	1199	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	82.247	743	1199	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	79.8449	520	1199	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	79.7646	548	1199	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	78.6894	424	1199	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.5202	356	1199	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.5079	383	1199	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.3304	380	1199	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.3258	381	1199	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.2703	383	1199	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	78.2475	422	1199	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.0195	300	1199	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.6286	236	1199	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.4544	187	1199	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.288	248	1199	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0707	251	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:58,282] [INFO] DFAST Taxonomy check result was written to GCF_001418085.1_ASM141808v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:58,282] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:58,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:58,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference/checkm_data
[2024-01-25 18:43:58,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:58,321] [INFO] Task started: CheckM
[2024-01-25 18:43:58,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418085.1_ASM141808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418085.1_ASM141808v1_genomic.fna/checkm_input GCF_001418085.1_ASM141808v1_genomic.fna/checkm_result
[2024-01-25 18:44:25,430] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:25,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:25,448] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:25,448] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:25,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418085.1_ASM141808v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:25,449] [INFO] Task started: Blastn
[2024-01-25 18:44:25,450] [INFO] Running command: blastn -query GCF_001418085.1_ASM141808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc2763fd-3f51-4f24-8747-8828ee18c462/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418085.1_ASM141808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:26,380] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:26,382] [INFO] Selected 10 target genomes.
[2024-01-25 18:44:26,383] [INFO] Target genome list was writen to GCF_001418085.1_ASM141808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:26,388] [INFO] Task started: fastANI
[2024-01-25 18:44:26,388] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2b9b948-d048-4b1e-8a49-862cbae6c21e/GCF_001418085.1_ASM141808v1_genomic.fna.gz --refList GCF_001418085.1_ASM141808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418085.1_ASM141808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:35,139] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:35,149] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:35,149] [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_001418085.1	s__Lacinutrix algicola	100.0	1193	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001418015.1	s__Lacinutrix mariniflava	87.2932	955	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831665.1	s__Lacinutrix sp002831665	86.7221	881	1199	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	82.255	741	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	81.7748	697	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	80.5911	612	1199	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	80.4597	634	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	78.4872	393	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.2722	384	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900112595.1	s__Algibacter_B pectinivorans	77.9677	344	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:35,153] [INFO] GTDB search result was written to GCF_001418085.1_ASM141808v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:35,154] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:35,157] [INFO] DFAST_QC result json was written to GCF_001418085.1_ASM141808v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:35,157] [INFO] DFAST_QC completed!
[2024-01-25 18:44:35,157] [INFO] Total running time: 0h0m60s