[2023-03-15 03:51:12,305] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:51:12,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:51:12,305] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference
[2023-03-15 03:51:13,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:51:13,391] [INFO] Task started: Prodigal
[2023-03-15 03:51:13,391] [INFO] Running command: cat /var/lib/cwl/stg3a5890c9-79aa-477d-bf0c-db6b57f4c469/OceanDNA-b6769.fa | prodigal -d OceanDNA-b6769/cds.fna -a OceanDNA-b6769/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:51:27,022] [INFO] Task succeeded: Prodigal
[2023-03-15 03:51:27,023] [INFO] Task started: HMMsearch
[2023-03-15 03:51:27,023] [INFO] Running command: hmmsearch --tblout OceanDNA-b6769/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference/reference_markers.hmm OceanDNA-b6769/protein.faa > /dev/null
[2023-03-15 03:51:27,210] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:51:27,211] [INFO] Found 6/6 markers.
[2023-03-15 03:51:27,228] [INFO] Query marker FASTA was written to OceanDNA-b6769/markers.fasta
[2023-03-15 03:51:27,229] [INFO] Task started: Blastn
[2023-03-15 03:51:27,229] [INFO] Running command: blastn -query OceanDNA-b6769/markers.fasta -db /var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference/reference_markers.fasta -out OceanDNA-b6769/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:51:27,873] [INFO] Task succeeded: Blastn
[2023-03-15 03:51:27,875] [INFO] Selected 19 target genomes.
[2023-03-15 03:51:27,875] [INFO] Target genome list was writen to OceanDNA-b6769/target_genomes.txt
[2023-03-15 03:51:27,897] [INFO] Task started: fastANI
[2023-03-15 03:51:27,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5890c9-79aa-477d-bf0c-db6b57f4c469/OceanDNA-b6769.fa --refList OceanDNA-b6769/target_genomes.txt --output OceanDNA-b6769/fastani_result.tsv --threads 1
[2023-03-15 03:51:42,276] [INFO] Task succeeded: fastANI
[2023-03-15 03:51:42,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:51:42,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:51:42,288] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:51:42,288] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:51:42,288] [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
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	80.9399	418	639	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	80.5162	422	639	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	80.2844	389	639	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	80.12	418	639	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	79.7335	381	639	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.5868	344	639	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.5397	374	639	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.4701	362	639	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	79.3252	332	639	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	79.2707	335	639	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	79.1346	321	639	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	79.1308	318	639	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.8087	285	639	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	78.4261	259	639	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	78.3812	241	639	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.0637	218	639	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.2985	94	639	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.1127	74	639	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.6524	66	639	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:51:42,289] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6769/tc_result.tsv
[2023-03-15 03:51:42,289] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:51:42,289] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:51:42,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference/checkm_data
[2023-03-15 03:51:42,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:51:42,294] [INFO] Task started: CheckM
[2023-03-15 03:51:42,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6769/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6769/checkm_input OceanDNA-b6769/checkm_result
[2023-03-15 03:52:19,993] [INFO] Task succeeded: CheckM
[2023-03-15 03:52:19,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:52:19,996] [INFO] ===== Completeness check finished =====
[2023-03-15 03:52:19,997] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:52:19,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6769/markers.fasta)
[2023-03-15 03:52:19,998] [INFO] Task started: Blastn
[2023-03-15 03:52:19,998] [INFO] Running command: blastn -query OceanDNA-b6769/markers.fasta -db /var/lib/cwl/stgb5fa9dd8-a05c-4a53-bbfa-225a00798fe7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6769/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:52:20,913] [INFO] Task succeeded: Blastn
[2023-03-15 03:52:20,916] [INFO] Selected 16 target genomes.
[2023-03-15 03:52:20,916] [INFO] Target genome list was writen to OceanDNA-b6769/target_genomes_gtdb.txt
[2023-03-15 03:52:20,932] [INFO] Task started: fastANI
[2023-03-15 03:52:20,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5890c9-79aa-477d-bf0c-db6b57f4c469/OceanDNA-b6769.fa --refList OceanDNA-b6769/target_genomes_gtdb.txt --output OceanDNA-b6769/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:52:31,109] [INFO] Task succeeded: fastANI
[2023-03-15 03:52:31,118] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:52:31,118] [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_002413745.1	s__Flavobacterium sp002413745	82.804	474	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCA_903861155.1	s__Flavobacterium sp903861155	82.7434	418	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCF_015277675.1	s__Flavobacterium soyangense	82.0209	472	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837155.1	s__Flavobacterium sp012837155	81.5234	424	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	81.0421	302	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	80.9502	417	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_014379405.1	s__Flavobacterium sp014379405	80.8038	363	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	80.5953	397	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	80.2936	388	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	80.1002	420	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355225.1	s__Flavobacterium nackdongense	79.758	379	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634825.1	s__Flavobacterium sp003634825	79.3858	337	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	79.3709	354	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_003634755.1	s__Flavobacterium limicola	79.3107	333	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668995.1	s__Flavobacterium sp003668995	78.4624	241	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	77.8893	196	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:52:31,120] [INFO] GTDB search result was written to OceanDNA-b6769/result_gtdb.tsv
[2023-03-15 03:52:31,123] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:52:31,126] [INFO] DFAST_QC result json was written to OceanDNA-b6769/dqc_result.json
[2023-03-15 03:52:31,126] [INFO] DFAST_QC completed!
[2023-03-15 03:52:31,126] [INFO] Total running time: 0h1m19s