[2024-01-25 18:12:05,748] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:05,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:05,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference
[2024-01-25 18:12:06,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:06,894] [INFO] Task started: Prodigal
[2024-01-25 18:12:06,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg18fc04cd-c641-4f80-a4ec-f511d3f87e29/GCF_014635865.1_ASM1463586v1_genomic.fna.gz | prodigal -d GCF_014635865.1_ASM1463586v1_genomic.fna/cds.fna -a GCF_014635865.1_ASM1463586v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:14,929] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:14,929] [INFO] Task started: HMMsearch
[2024-01-25 18:12:14,929] [INFO] Running command: hmmsearch --tblout GCF_014635865.1_ASM1463586v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference/reference_markers.hmm GCF_014635865.1_ASM1463586v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:15,156] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:15,158] [INFO] Found 6/6 markers.
[2024-01-25 18:12:15,184] [INFO] Query marker FASTA was written to GCF_014635865.1_ASM1463586v1_genomic.fna/markers.fasta
[2024-01-25 18:12:15,184] [INFO] Task started: Blastn
[2024-01-25 18:12:15,184] [INFO] Running command: blastn -query GCF_014635865.1_ASM1463586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference/reference_markers.fasta -out GCF_014635865.1_ASM1463586v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:15,819] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:15,822] [INFO] Selected 18 target genomes.
[2024-01-25 18:12:15,822] [INFO] Target genome list was writen to GCF_014635865.1_ASM1463586v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:15,833] [INFO] Task started: fastANI
[2024-01-25 18:12:15,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg18fc04cd-c641-4f80-a4ec-f511d3f87e29/GCF_014635865.1_ASM1463586v1_genomic.fna.gz --refList GCF_014635865.1_ASM1463586v1_genomic.fna/target_genomes.txt --output GCF_014635865.1_ASM1463586v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:27,375] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:27,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:27,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:27,387] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:27,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:27,387] [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 haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	100.0	1011	1011	95	conclusive
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	80.1741	613	1011	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	79.5422	519	1011	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.3752	380	1011	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.3648	381	1011	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.1007	262	1011	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.0058	329	1011	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.9974	329	1011	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.9466	286	1011	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.9381	327	1011	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.9092	303	1011	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.8308	283	1011	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	77.8231	240	1011	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.679	271	1011	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.6031	143	1011	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.3032	166	1011	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.1549	125	1011	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.9308	145	1011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:27,389] [INFO] DFAST Taxonomy check result was written to GCF_014635865.1_ASM1463586v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:27,389] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:27,389] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:27,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference/checkm_data
[2024-01-25 18:12:27,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:27,422] [INFO] Task started: CheckM
[2024-01-25 18:12:27,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635865.1_ASM1463586v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635865.1_ASM1463586v1_genomic.fna/checkm_input GCF_014635865.1_ASM1463586v1_genomic.fna/checkm_result
[2024-01-25 18:12:55,793] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:55,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:55,816] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:55,816] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:55,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635865.1_ASM1463586v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:55,817] [INFO] Task started: Blastn
[2024-01-25 18:12:55,817] [INFO] Running command: blastn -query GCF_014635865.1_ASM1463586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2044dceb-ceec-4726-86ea-b3f135ee679e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635865.1_ASM1463586v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:56,778] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:56,781] [INFO] Selected 11 target genomes.
[2024-01-25 18:12:56,781] [INFO] Target genome list was writen to GCF_014635865.1_ASM1463586v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:56,796] [INFO] Task started: fastANI
[2024-01-25 18:12:56,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg18fc04cd-c641-4f80-a4ec-f511d3f87e29/GCF_014635865.1_ASM1463586v1_genomic.fna.gz --refList GCF_014635865.1_ASM1463586v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635865.1_ASM1463586v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:04,270] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:04,277] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:04,277] [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_014635865.1	s__Winogradskyella haliclonae	100.0	1011	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004211785.1	s__Winogradskyella sp004211785	84.3867	697	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	80.1746	613	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163855.1	s__Winogradskyella sp002163855	80.104	592	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCA_905480385.1	s__Winogradskyella sp905480385	79.7674	435	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCA_013042245.1	s__Winogradskyella sp013042245	79.6955	416	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_004346845.1	s__Winogradskyella wandonensis	79.5465	521	1011	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	78.3242	265	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.1627	366	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	78.01	327	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	77.9974	329	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:04,279] [INFO] GTDB search result was written to GCF_014635865.1_ASM1463586v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:04,279] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:04,282] [INFO] DFAST_QC result json was written to GCF_014635865.1_ASM1463586v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:04,282] [INFO] DFAST_QC completed!
[2024-01-25 18:13:04,282] [INFO] Total running time: 0h0m59s