[2024-01-24 14:30:59,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference
[2024-01-24 14:31:00,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,670] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,670] [INFO] Running command: gunzip -c /var/lib/cwl/stgde56161a-add4-49f9-99b4-9441739dfb3a/GCF_019203985.1_ASM1920398v1_genomic.fna.gz | prodigal -d GCF_019203985.1_ASM1920398v1_genomic.fna/cds.fna -a GCF_019203985.1_ASM1920398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:12,849] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:12,849] [INFO] Task started: HMMsearch
[2024-01-24 14:31:12,849] [INFO] Running command: hmmsearch --tblout GCF_019203985.1_ASM1920398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference/reference_markers.hmm GCF_019203985.1_ASM1920398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:13,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:13,188] [INFO] Found 6/6 markers.
[2024-01-24 14:31:13,222] [INFO] Query marker FASTA was written to GCF_019203985.1_ASM1920398v1_genomic.fna/markers.fasta
[2024-01-24 14:31:13,222] [INFO] Task started: Blastn
[2024-01-24 14:31:13,222] [INFO] Running command: blastn -query GCF_019203985.1_ASM1920398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference/reference_markers.fasta -out GCF_019203985.1_ASM1920398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:13,928] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:13,933] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:13,933] [INFO] Target genome list was writen to GCF_019203985.1_ASM1920398v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:13,943] [INFO] Task started: fastANI
[2024-01-24 14:31:13,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgde56161a-add4-49f9-99b4-9441739dfb3a/GCF_019203985.1_ASM1920398v1_genomic.fna.gz --refList GCF_019203985.1_ASM1920398v1_genomic.fna/target_genomes.txt --output GCF_019203985.1_ASM1920398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:26,180] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:26,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:26,266] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:26,267] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:26,268] [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 ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	79.5406	553	1156	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	79.1127	540	1156	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.0978	502	1156	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.0843	504	1156	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.9302	523	1156	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	78.8436	184	1156	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.5794	376	1156	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.562	439	1156	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.3635	395	1156	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.287	421	1156	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.167	392	1156	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	78.0836	362	1156	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.7086	288	1156	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.6693	301	1156	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.6484	158	1156	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.5924	260	1156	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.287	160	1156	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2609	207	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,270] [INFO] DFAST Taxonomy check result was written to GCF_019203985.1_ASM1920398v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:26,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:26,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:26,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference/checkm_data
[2024-01-24 14:31:26,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:26,315] [INFO] Task started: CheckM
[2024-01-24 14:31:26,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019203985.1_ASM1920398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019203985.1_ASM1920398v1_genomic.fna/checkm_input GCF_019203985.1_ASM1920398v1_genomic.fna/checkm_result
[2024-01-24 14:32:05,693] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:05,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:05,718] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:05,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:05,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019203985.1_ASM1920398v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:05,719] [INFO] Task started: Blastn
[2024-01-24 14:32:05,719] [INFO] Running command: blastn -query GCF_019203985.1_ASM1920398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76ecb323-ef2f-4b96-afc9-c8f8f831e73b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019203985.1_ASM1920398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:06,682] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:06,686] [INFO] Selected 17 target genomes.
[2024-01-24 14:32:06,686] [INFO] Target genome list was writen to GCF_019203985.1_ASM1920398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:06,700] [INFO] Task started: fastANI
[2024-01-24 14:32:06,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgde56161a-add4-49f9-99b4-9441739dfb3a/GCF_019203985.1_ASM1920398v1_genomic.fna.gz --refList GCF_019203985.1_ASM1920398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019203985.1_ASM1920398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:18,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:18,597] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:18,598] [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_019203985.1	s__Winogradskyella sp019203985	100.0	1152	1156	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_009709615.1	s__Winogradskyella ouciana	79.55	552	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	79.178	511	1156	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	79.1397	505	1156	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	79.0991	541	1156	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	79.0937	503	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869935.1	s__Winogradskyella algicola	78.9463	522	1156	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	78.9309	497	1156	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	78.885	409	1156	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	78.7908	465	1156	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	78.5752	377	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.5615	439	1156	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	78.4414	415	1156	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	78.3416	422	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	78.2901	420	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	77.9986	264	1156	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	77.7114	289	1156	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 14:32:18,599] [INFO] GTDB search result was written to GCF_019203985.1_ASM1920398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:18,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:18,604] [INFO] DFAST_QC result json was written to GCF_019203985.1_ASM1920398v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:18,605] [INFO] DFAST_QC completed!
[2024-01-24 14:32:18,605] [INFO] Total running time: 0h1m19s