[2023-06-19 05:24:43,022] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:24:43,028] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:24:43,028] [INFO] DQC Reference Directory: /var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference
[2023-06-19 05:24:44,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:24:44,594] [INFO] Task started: Prodigal
[2023-06-19 05:24:44,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgb62ea45e-13a1-4c3d-9586-cdde5530da3e/GCA_013213975.1_ASM1321397v1_genomic.fna.gz | prodigal -d GCA_013213975.1_ASM1321397v1_genomic.fna/cds.fna -a GCA_013213975.1_ASM1321397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:24:54,134] [INFO] Task succeeded: Prodigal
[2023-06-19 05:24:54,134] [INFO] Task started: HMMsearch
[2023-06-19 05:24:54,134] [INFO] Running command: hmmsearch --tblout GCA_013213975.1_ASM1321397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference/reference_markers.hmm GCA_013213975.1_ASM1321397v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:24:54,419] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:24:54,420] [INFO] Found 6/6 markers.
[2023-06-19 05:24:54,456] [INFO] Query marker FASTA was written to GCA_013213975.1_ASM1321397v1_genomic.fna/markers.fasta
[2023-06-19 05:24:54,457] [INFO] Task started: Blastn
[2023-06-19 05:24:54,457] [INFO] Running command: blastn -query GCA_013213975.1_ASM1321397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference/reference_markers.fasta -out GCA_013213975.1_ASM1321397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:24:55,156] [INFO] Task succeeded: Blastn
[2023-06-19 05:24:55,163] [INFO] Selected 23 target genomes.
[2023-06-19 05:24:55,163] [INFO] Target genome list was writen to GCA_013213975.1_ASM1321397v1_genomic.fna/target_genomes.txt
[2023-06-19 05:24:55,170] [INFO] Task started: fastANI
[2023-06-19 05:24:55,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62ea45e-13a1-4c3d-9586-cdde5530da3e/GCA_013213975.1_ASM1321397v1_genomic.fna.gz --refList GCA_013213975.1_ASM1321397v1_genomic.fna/target_genomes.txt --output GCA_013213975.1_ASM1321397v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:10,212] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:10,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:10,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:10,236] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:10,236] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:25:10,237] [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	78.4891	381	959	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.2992	370	959	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	78.2833	350	959	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.2765	356	959	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.2765	356	959	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.1462	377	959	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.0567	256	959	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.8511	279	959	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.8489	271	959	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.815	276	959	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.8042	242	959	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.7662	277	959	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	77.7484	264	959	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.7271	295	959	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.7217	219	959	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.7212	290	959	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	77.7197	260	959	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.3228	187	959	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.1574	122	959	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.0422	78	959	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.8789	118	959	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.8769	56	959	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:25:10,246] [INFO] DFAST Taxonomy check result was written to GCA_013213975.1_ASM1321397v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:10,247] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:10,247] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:10,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference/checkm_data
[2023-06-19 05:25:10,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:10,284] [INFO] Task started: CheckM
[2023-06-19 05:25:10,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013213975.1_ASM1321397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013213975.1_ASM1321397v1_genomic.fna/checkm_input GCA_013213975.1_ASM1321397v1_genomic.fna/checkm_result
[2023-06-19 05:25:42,695] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:42,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:42,735] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:42,736] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:42,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013213975.1_ASM1321397v1_genomic.fna/markers.fasta)
[2023-06-19 05:25:42,736] [INFO] Task started: Blastn
[2023-06-19 05:25:42,736] [INFO] Running command: blastn -query GCA_013213975.1_ASM1321397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf977ba8b-18a0-42f2-a28a-e495ff40d6c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_013213975.1_ASM1321397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:43,628] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:43,634] [INFO] Selected 18 target genomes.
[2023-06-19 05:25:43,634] [INFO] Target genome list was writen to GCA_013213975.1_ASM1321397v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:43,647] [INFO] Task started: fastANI
[2023-06-19 05:25:43,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgb62ea45e-13a1-4c3d-9586-cdde5530da3e/GCA_013213975.1_ASM1321397v1_genomic.fna.gz --refList GCA_013213975.1_ASM1321397v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013213975.1_ASM1321397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:25:54,922] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:54,943] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:25:54,943] [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
GCA_013213975.1	s__Winogradskyella sp013213975	100.0	950	959	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	78.6158	317	959	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	78.4917	382	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.4203	338	959	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	78.3601	355	959	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	78.3394	356	959	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	78.3347	350	959	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	78.2992	370	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_003260205.1	s__Winogradskyella tangerina	78.2872	349	959	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	78.2697	356	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014243395.1	s__Winogradskyella flava	78.1475	377	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335675.1	s__Winogradskyella sp003335675	78.1039	285	959	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	78.0158	319	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	77.9468	267	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_003386165.1	s__Winogradskyella eximia	77.9396	263	959	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	77.8653	338	959	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	77.8059	276	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.2541	180	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-19 05:25:54,945] [INFO] GTDB search result was written to GCA_013213975.1_ASM1321397v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:25:54,946] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:25:54,954] [INFO] DFAST_QC result json was written to GCA_013213975.1_ASM1321397v1_genomic.fna/dqc_result.json
[2023-06-19 05:25:54,954] [INFO] DFAST_QC completed!
[2023-06-19 05:25:54,955] [INFO] Total running time: 0h1m12s