[2024-01-25 18:42:50,472] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,473] [INFO] DQC Reference Directory: /var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference
[2024-01-25 18:42:51,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:51,640] [INFO] Task started: Prodigal
[2024-01-25 18:42:51,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0d84f2b-2ed5-4c9f-8cfc-85c17ccc6b7f/GCF_020166335.1_ASM2016633v1_genomic.fna.gz | prodigal -d GCF_020166335.1_ASM2016633v1_genomic.fna/cds.fna -a GCF_020166335.1_ASM2016633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:01,306] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:01,306] [INFO] Task started: HMMsearch
[2024-01-25 18:43:01,306] [INFO] Running command: hmmsearch --tblout GCF_020166335.1_ASM2016633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference/reference_markers.hmm GCF_020166335.1_ASM2016633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:01,548] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:01,549] [INFO] Found 6/6 markers.
[2024-01-25 18:43:01,577] [INFO] Query marker FASTA was written to GCF_020166335.1_ASM2016633v1_genomic.fna/markers.fasta
[2024-01-25 18:43:01,577] [INFO] Task started: Blastn
[2024-01-25 18:43:01,577] [INFO] Running command: blastn -query GCF_020166335.1_ASM2016633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference/reference_markers.fasta -out GCF_020166335.1_ASM2016633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:02,187] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:02,193] [INFO] Selected 29 target genomes.
[2024-01-25 18:43:02,194] [INFO] Target genome list was writen to GCF_020166335.1_ASM2016633v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:02,216] [INFO] Task started: fastANI
[2024-01-25 18:43:02,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d84f2b-2ed5-4c9f-8cfc-85c17ccc6b7f/GCF_020166335.1_ASM2016633v1_genomic.fna.gz --refList GCF_020166335.1_ASM2016633v1_genomic.fna/target_genomes.txt --output GCF_020166335.1_ASM2016633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:20,905] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:20,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:20,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:20,925] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:43:20,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:43:20,925] [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	78.173	335	1086	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.1028	266	1086	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.8912	299	1086	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.8187	229	1086	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.7717	309	1086	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.7717	309	1086	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	77.7122	286	1086	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	77.6569	162	1086	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	77.609	267	1086	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	77.5976	219	1086	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.5818	235	1086	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.5602	254	1086	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.5541	231	1086	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.5435	237	1086	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.5198	218	1086	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.3736	154	1086	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.3732	309	1086	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.3595	155	1086	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.3298	220	1086	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.323	107	1086	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	77.3204	130	1086	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.2825	176	1086	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	77.2421	230	1086	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.2292	124	1086	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.9526	189	1086	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.7994	126	1086	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	76.7442	88	1086	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.6928	141	1086	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.635	81	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:20,928] [INFO] DFAST Taxonomy check result was written to GCF_020166335.1_ASM2016633v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:20,928] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:20,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:20,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference/checkm_data
[2024-01-25 18:43:20,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:20,966] [INFO] Task started: CheckM
[2024-01-25 18:43:20,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020166335.1_ASM2016633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020166335.1_ASM2016633v1_genomic.fna/checkm_input GCF_020166335.1_ASM2016633v1_genomic.fna/checkm_result
[2024-01-25 18:43:52,576] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:52,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:52,597] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:52,597] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:52,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020166335.1_ASM2016633v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:52,598] [INFO] Task started: Blastn
[2024-01-25 18:43:52,598] [INFO] Running command: blastn -query GCF_020166335.1_ASM2016633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga529be62-0522-4e65-ab78-3fedb373301f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020166335.1_ASM2016633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:53,486] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:53,489] [INFO] Selected 19 target genomes.
[2024-01-25 18:43:53,489] [INFO] Target genome list was writen to GCF_020166335.1_ASM2016633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:53,502] [INFO] Task started: fastANI
[2024-01-25 18:43:53,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d84f2b-2ed5-4c9f-8cfc-85c17ccc6b7f/GCF_020166335.1_ASM2016633v1_genomic.fna.gz --refList GCF_020166335.1_ASM2016633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020166335.1_ASM2016633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:04,994] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:05,009] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:44:05,009] [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_003335675.1	s__Winogradskyella sp003335675	78.9423	468	1086	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	78.3973	273	1086	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	78.1616	336	1086	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	78.0985	267	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_019203985.1	s__Winogradskyella sp019203985	77.9416	295	1086	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	77.9029	298	1086	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	77.8039	267	1086	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	77.8024	325	1086	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	77.7905	313	1086	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	77.761	310	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.6476	287	1086	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	77.6145	270	1086	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	77.4713	177	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.3971	178	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_013002225.1	s__Winogradskyella sp013002225	77.3853	235	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358095.2	s__Seonamhaeicola sp004358095	77.3333	157	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.298	152	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	77.0202	135	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.8605	191	1086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:05,010] [INFO] GTDB search result was written to GCF_020166335.1_ASM2016633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:05,011] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:05,015] [INFO] DFAST_QC result json was written to GCF_020166335.1_ASM2016633v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:05,016] [INFO] DFAST_QC completed!
[2024-01-25 18:44:05,016] [INFO] Total running time: 0h1m15s