[2024-01-24 12:29:21,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:21,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:21,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference
[2024-01-24 12:29:22,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:22,395] [INFO] Task started: Prodigal
[2024-01-24 12:29:22,395] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb605185-3db1-4aa8-be72-a500916004e3/GCF_014284085.1_ASM1428408v1_genomic.fna.gz | prodigal -d GCF_014284085.1_ASM1428408v1_genomic.fna/cds.fna -a GCF_014284085.1_ASM1428408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:33,513] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:33,514] [INFO] Task started: HMMsearch
[2024-01-24 12:29:33,514] [INFO] Running command: hmmsearch --tblout GCF_014284085.1_ASM1428408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference/reference_markers.hmm GCF_014284085.1_ASM1428408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:33,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:33,801] [INFO] Found 6/6 markers.
[2024-01-24 12:29:33,835] [INFO] Query marker FASTA was written to GCF_014284085.1_ASM1428408v1_genomic.fna/markers.fasta
[2024-01-24 12:29:33,835] [INFO] Task started: Blastn
[2024-01-24 12:29:33,836] [INFO] Running command: blastn -query GCF_014284085.1_ASM1428408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference/reference_markers.fasta -out GCF_014284085.1_ASM1428408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:34,499] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:34,502] [INFO] Selected 15 target genomes.
[2024-01-24 12:29:34,502] [INFO] Target genome list was writen to GCF_014284085.1_ASM1428408v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:34,515] [INFO] Task started: fastANI
[2024-01-24 12:29:34,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb605185-3db1-4aa8-be72-a500916004e3/GCF_014284085.1_ASM1428408v1_genomic.fna.gz --refList GCF_014284085.1_ASM1428408v1_genomic.fna/target_genomes.txt --output GCF_014284085.1_ASM1428408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:45,764] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:45,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:45,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:45,777] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:29:45,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:45,778] [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 echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	100.0	1255	1256	95	conclusive
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	100.0	1255	1256	95	conclusive
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	80.2674	656	1256	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	79.7963	580	1256	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	79.6844	627	1256	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	79.6765	660	1256	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	79.6327	643	1256	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	79.1043	523	1256	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	79.0001	567	1256	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.9017	542	1256	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.737	328	1256	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.0811	214	1256	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0746	209	1256	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0592	239	1256	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.5174	119	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:45,779] [INFO] DFAST Taxonomy check result was written to GCF_014284085.1_ASM1428408v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:45,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:45,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:45,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference/checkm_data
[2024-01-24 12:29:45,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:45,824] [INFO] Task started: CheckM
[2024-01-24 12:29:45,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284085.1_ASM1428408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284085.1_ASM1428408v1_genomic.fna/checkm_input GCF_014284085.1_ASM1428408v1_genomic.fna/checkm_result
[2024-01-24 12:30:21,580] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:21,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:21,604] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:21,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:21,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284085.1_ASM1428408v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:21,605] [INFO] Task started: Blastn
[2024-01-24 12:30:21,606] [INFO] Running command: blastn -query GCF_014284085.1_ASM1428408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635a32ea-42b9-4824-900d-85f5bafce4ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284085.1_ASM1428408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:22,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:22,544] [INFO] Selected 14 target genomes.
[2024-01-24 12:30:22,544] [INFO] Target genome list was writen to GCF_014284085.1_ASM1428408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:22,555] [INFO] Task started: fastANI
[2024-01-24 12:30:22,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb605185-3db1-4aa8-be72-a500916004e3/GCF_014284085.1_ASM1428408v1_genomic.fna.gz --refList GCF_014284085.1_ASM1428408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284085.1_ASM1428408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:33,764] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:33,789] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:33,789] [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_014297365.1	s__Winogradskyella echinorum	100.0	1255	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_000171875.1	s__Winogradskyella sp000171875	81.9594	793	1256	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	80.6842	677	1256	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	80.5309	722	1256	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	80.2585	658	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	80.2179	664	1256	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	80.1627	661	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	79.705	623	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	79.6169	645	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCA_002364335.1	s__Winogradskyella sp002364335	79.4968	570	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	79.2449	501	1256	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403955.1	s__Winogradskyella vidalii	79.0997	524	1256	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	79.0048	567	1256	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	78.8226	518	1256	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 12:30:33,793] [INFO] GTDB search result was written to GCF_014284085.1_ASM1428408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:33,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:33,800] [INFO] DFAST_QC result json was written to GCF_014284085.1_ASM1428408v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:33,800] [INFO] DFAST_QC completed!
[2024-01-24 12:30:33,800] [INFO] Total running time: 0h1m13s