[2024-01-24 12:23:04,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference
[2024-01-24 12:23:05,281] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,282] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c62511b-ae42-46e5-aedd-ce5460728789/GCF_014243395.1_ASM1424339v1_genomic.fna.gz | prodigal -d GCF_014243395.1_ASM1424339v1_genomic.fna/cds.fna -a GCF_014243395.1_ASM1424339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:18,908] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:18,909] [INFO] Task started: HMMsearch
[2024-01-24 12:23:18,909] [INFO] Running command: hmmsearch --tblout GCF_014243395.1_ASM1424339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference/reference_markers.hmm GCF_014243395.1_ASM1424339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:19,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:19,182] [INFO] Found 6/6 markers.
[2024-01-24 12:23:19,218] [INFO] Query marker FASTA was written to GCF_014243395.1_ASM1424339v1_genomic.fna/markers.fasta
[2024-01-24 12:23:19,219] [INFO] Task started: Blastn
[2024-01-24 12:23:19,219] [INFO] Running command: blastn -query GCF_014243395.1_ASM1424339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference/reference_markers.fasta -out GCF_014243395.1_ASM1424339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,960] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,963] [INFO] Selected 21 target genomes.
[2024-01-24 12:23:19,964] [INFO] Target genome list was writen to GCF_014243395.1_ASM1424339v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:19,974] [INFO] Task started: fastANI
[2024-01-24 12:23:19,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c62511b-ae42-46e5-aedd-ce5460728789/GCF_014243395.1_ASM1424339v1_genomic.fna.gz --refList GCF_014243395.1_ASM1424339v1_genomic.fna/target_genomes.txt --output GCF_014243395.1_ASM1424339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:34,529] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:34,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:34,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:34,551] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:34,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:34,551] [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 flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	100.0	1281	1281	95	conclusive
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	79.2077	531	1281	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.7924	549	1281	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.7844	550	1281	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.6616	481	1281	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.2194	386	1281	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.1548	400	1281	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	78.0979	419	1281	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	78.0779	411	1281	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.046	363	1281	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.0418	421	1281	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.0232	384	1281	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.8899	306	1281	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.8854	327	1281	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.8489	349	1281	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.1714	187	1281	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.1709	160	1281	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.0563	190	1281	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9652	178	1281	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.9613	202	1281	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.9515	58	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:34,553] [INFO] DFAST Taxonomy check result was written to GCF_014243395.1_ASM1424339v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:34,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:34,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:34,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference/checkm_data
[2024-01-24 12:23:34,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:34,597] [INFO] Task started: CheckM
[2024-01-24 12:23:34,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014243395.1_ASM1424339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014243395.1_ASM1424339v1_genomic.fna/checkm_input GCF_014243395.1_ASM1424339v1_genomic.fna/checkm_result
[2024-01-24 12:24:16,326] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:16,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:16,350] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:16,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:16,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014243395.1_ASM1424339v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:16,351] [INFO] Task started: Blastn
[2024-01-24 12:24:16,351] [INFO] Running command: blastn -query GCF_014243395.1_ASM1424339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29f4cf5b-8b61-489d-afbf-785f70f63736/dqc_reference/reference_markers_gtdb.fasta -out GCF_014243395.1_ASM1424339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:17,269] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:17,273] [INFO] Selected 15 target genomes.
[2024-01-24 12:24:17,274] [INFO] Target genome list was writen to GCF_014243395.1_ASM1424339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:17,285] [INFO] Task started: fastANI
[2024-01-24 12:24:17,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c62511b-ae42-46e5-aedd-ce5460728789/GCF_014243395.1_ASM1424339v1_genomic.fna.gz --refList GCF_014243395.1_ASM1424339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014243395.1_ASM1424339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:27,170] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:27,187] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:27,187] [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_014243395.1	s__Winogradskyella flava	100.0	1281	1281	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	79.2161	530	1281	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	79.1208	566	1281	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	79.0574	549	1281	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	78.9939	500	1281	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	78.7849	550	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002722255.1	s__Winogradskyella sp002722255	78.7509	393	1281	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	78.6657	480	1281	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	78.4579	456	1281	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	78.4523	453	1281	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	78.1584	411	1281	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	78.1261	367	1281	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	78.0654	361	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_905480385.1	s__Winogradskyella sp905480385	77.7282	233	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.0679	189	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:27,189] [INFO] GTDB search result was written to GCF_014243395.1_ASM1424339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:27,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:27,193] [INFO] DFAST_QC result json was written to GCF_014243395.1_ASM1424339v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:27,193] [INFO] DFAST_QC completed!
[2024-01-24 12:24:27,193] [INFO] Total running time: 0h1m23s