[2024-01-24 14:06:05,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference
[2024-01-24 14:06:06,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:06,775] [INFO] Task started: Prodigal
[2024-01-24 14:06:06,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg49d7ade7-9dbf-4559-b854-e9e1036642c1/GCF_005869935.1_ASM586993v1_genomic.fna.gz | prodigal -d GCF_005869935.1_ASM586993v1_genomic.fna/cds.fna -a GCF_005869935.1_ASM586993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:18,203] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:18,204] [INFO] Task started: HMMsearch
[2024-01-24 14:06:18,204] [INFO] Running command: hmmsearch --tblout GCF_005869935.1_ASM586993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference/reference_markers.hmm GCF_005869935.1_ASM586993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:18,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:18,527] [INFO] Found 6/6 markers.
[2024-01-24 14:06:18,572] [INFO] Query marker FASTA was written to GCF_005869935.1_ASM586993v1_genomic.fna/markers.fasta
[2024-01-24 14:06:18,573] [INFO] Task started: Blastn
[2024-01-24 14:06:18,573] [INFO] Running command: blastn -query GCF_005869935.1_ASM586993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference/reference_markers.fasta -out GCF_005869935.1_ASM586993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,344] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:19,344] [INFO] Target genome list was writen to GCF_005869935.1_ASM586993v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:19,359] [INFO] Task started: fastANI
[2024-01-24 14:06:19,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d7ade7-9dbf-4559-b854-e9e1036642c1/GCF_005869935.1_ASM586993v1_genomic.fna.gz --refList GCF_005869935.1_ASM586993v1_genomic.fna/target_genomes.txt --output GCF_005869935.1_ASM586993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:32,232] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:32,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:32,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:32,247] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:32,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:32,247] [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
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	100.0	1106	1107	95	conclusive
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	79.3728	517	1107	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.1337	520	1107	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.1337	520	1107	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.7679	452	1107	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.7434	471	1107	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.6035	409	1107	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.5762	411	1107	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.5438	481	1107	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.3603	444	1107	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.2068	442	1107	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.7003	252	1107	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.419	226	1107	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.1684	192	1107	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0485	189	1107	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.6544	106	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,249] [INFO] DFAST Taxonomy check result was written to GCF_005869935.1_ASM586993v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:32,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:32,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:32,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference/checkm_data
[2024-01-24 14:06:32,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:32,286] [INFO] Task started: CheckM
[2024-01-24 14:06:32,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005869935.1_ASM586993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005869935.1_ASM586993v1_genomic.fna/checkm_input GCF_005869935.1_ASM586993v1_genomic.fna/checkm_result
[2024-01-24 14:07:08,706] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:08,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:08,727] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:08,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:08,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005869935.1_ASM586993v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:08,729] [INFO] Task started: Blastn
[2024-01-24 14:07:08,729] [INFO] Running command: blastn -query GCF_005869935.1_ASM586993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc375c7fd-93c0-48e1-ad28-3867c52ac976/dqc_reference/reference_markers_gtdb.fasta -out GCF_005869935.1_ASM586993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:09,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:09,765] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:09,765] [INFO] Target genome list was writen to GCF_005869935.1_ASM586993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:09,783] [INFO] Task started: fastANI
[2024-01-24 14:07:09,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d7ade7-9dbf-4559-b854-e9e1036642c1/GCF_005869935.1_ASM586993v1_genomic.fna.gz --refList GCF_005869935.1_ASM586993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005869935.1_ASM586993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:18,766] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:18,778] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:18,778] [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_005869935.1	s__Winogradskyella algicola	100.0	1106	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001971725.1	s__Winogradskyella sp001971725	89.8837	869	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	86.8673	705	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCA_002682935.1	s__Winogradskyella sp002682935	84.4182	777	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	79.368	517	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_014297365.1	s__Winogradskyella echinorum	79.1246	521	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019203985.1	s__Winogradskyella sp019203985	79.0829	508	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.8399	489	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243395.1	s__Winogradskyella flava	78.7525	470	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.6413	493	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213975.1	s__Winogradskyella sp013213975	78.5817	375	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	78.5663	439	1107	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:18,780] [INFO] GTDB search result was written to GCF_005869935.1_ASM586993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:18,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:18,784] [INFO] DFAST_QC result json was written to GCF_005869935.1_ASM586993v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:18,784] [INFO] DFAST_QC completed!
[2024-01-24 14:07:18,785] [INFO] Total running time: 0h1m13s