[2024-01-24 13:57:43,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,133] [INFO] DQC Reference Directory: /var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference
[2024-01-24 13:57:44,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,486] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,487] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e56a8ad-c5f3-40ab-b24e-82c79af0dc14/GCF_003260205.1_ASM326020v1_genomic.fna.gz | prodigal -d GCF_003260205.1_ASM326020v1_genomic.fna/cds.fna -a GCF_003260205.1_ASM326020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:57,060] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:57,060] [INFO] Task started: HMMsearch
[2024-01-24 13:57:57,060] [INFO] Running command: hmmsearch --tblout GCF_003260205.1_ASM326020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference/reference_markers.hmm GCF_003260205.1_ASM326020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,409] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,410] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,450] [INFO] Query marker FASTA was written to GCF_003260205.1_ASM326020v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,450] [INFO] Task started: Blastn
[2024-01-24 13:57:57,451] [INFO] Running command: blastn -query GCF_003260205.1_ASM326020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference/reference_markers.fasta -out GCF_003260205.1_ASM326020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,197] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,201] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:58,201] [INFO] Target genome list was writen to GCF_003260205.1_ASM326020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,207] [INFO] Task started: fastANI
[2024-01-24 13:57:58,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e56a8ad-c5f3-40ab-b24e-82c79af0dc14/GCF_003260205.1_ASM326020v1_genomic.fna.gz --refList GCF_003260205.1_ASM326020v1_genomic.fna/target_genomes.txt --output GCF_003260205.1_ASM326020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:11,781] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:11,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:11,796] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:11,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:11,797] [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 tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	100.0	1163	1164	95	conclusive
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.5932	433	1164	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.3569	411	1164	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.2408	440	1164	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.1034	386	1164	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1034	386	1164	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.7644	300	1164	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	77.7097	306	1164	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.6906	276	1164	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.6352	305	1164	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.5899	276	1164	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.3567	155	1164	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.1848	272	1164	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0282	139	1164	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.9975	103	1164	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.6887	150	1164	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.2388	70	1164	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.1999	50	1164	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,798] [INFO] DFAST Taxonomy check result was written to GCF_003260205.1_ASM326020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:11,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:11,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:11,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference/checkm_data
[2024-01-24 13:58:11,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:11,838] [INFO] Task started: CheckM
[2024-01-24 13:58:11,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003260205.1_ASM326020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003260205.1_ASM326020v1_genomic.fna/checkm_input GCF_003260205.1_ASM326020v1_genomic.fna/checkm_result
[2024-01-24 13:58:53,744] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:53,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,765] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:53,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:53,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003260205.1_ASM326020v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:53,766] [INFO] Task started: Blastn
[2024-01-24 13:58:53,766] [INFO] Running command: blastn -query GCF_003260205.1_ASM326020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceffc4e1-9c1e-411b-b553-6966dcc95f91/dqc_reference/reference_markers_gtdb.fasta -out GCF_003260205.1_ASM326020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:54,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:54,775] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:54,775] [INFO] Target genome list was writen to GCF_003260205.1_ASM326020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:54,794] [INFO] Task started: fastANI
[2024-01-24 13:58:54,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e56a8ad-c5f3-40ab-b24e-82c79af0dc14/GCF_003260205.1_ASM326020v1_genomic.fna.gz --refList GCF_003260205.1_ASM326020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003260205.1_ASM326020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:08,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:08,780] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:08,781] [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_003260205.1	s__Winogradskyella tangerina	100.0	1163	1164	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_002722255.1	s__Winogradskyella sp002722255	78.7462	352	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_005869935.1	s__Winogradskyella algicola	78.5932	433	1164	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	78.3569	411	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	78.3096	428	1164	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	78.2643	365	1164	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	78.2491	439	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.1441	425	1164	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	78.1122	383	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	78.1034	386	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.0091	377	1164	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	77.8686	356	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.8561	382	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394655.1	s__Winogradskyella schleiferi	77.7097	306	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	77.7047	274	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013403955.1	s__Winogradskyella vidalii	77.5899	276	1164	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	77.5202	312	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	77.4848	306	1164	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	77.1749	272	1164	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 13:59:08,782] [INFO] GTDB search result was written to GCF_003260205.1_ASM326020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:08,783] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:08,787] [INFO] DFAST_QC result json was written to GCF_003260205.1_ASM326020v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:08,787] [INFO] DFAST_QC completed!
[2024-01-24 13:59:08,787] [INFO] Total running time: 0h1m26s