[2024-01-24 11:05:34,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference
[2024-01-24 11:05:35,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,741] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg58d9f934-83eb-4463-8612-2935451c634c/GCF_020026915.1_ASM2002691v1_genomic.fna.gz | prodigal -d GCF_020026915.1_ASM2002691v1_genomic.fna/cds.fna -a GCF_020026915.1_ASM2002691v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:55,491] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:55,492] [INFO] Task started: HMMsearch
[2024-01-24 11:05:55,492] [INFO] Running command: hmmsearch --tblout GCF_020026915.1_ASM2002691v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference/reference_markers.hmm GCF_020026915.1_ASM2002691v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:55,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:55,885] [INFO] Found 6/6 markers.
[2024-01-24 11:05:55,932] [INFO] Query marker FASTA was written to GCF_020026915.1_ASM2002691v1_genomic.fna/markers.fasta
[2024-01-24 11:05:55,932] [INFO] Task started: Blastn
[2024-01-24 11:05:55,932] [INFO] Running command: blastn -query GCF_020026915.1_ASM2002691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference/reference_markers.fasta -out GCF_020026915.1_ASM2002691v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:56,636] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:56,640] [INFO] Selected 19 target genomes.
[2024-01-24 11:05:56,641] [INFO] Target genome list was writen to GCF_020026915.1_ASM2002691v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:56,649] [INFO] Task started: fastANI
[2024-01-24 11:05:56,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d9f934-83eb-4463-8612-2935451c634c/GCF_020026915.1_ASM2002691v1_genomic.fna.gz --refList GCF_020026915.1_ASM2002691v1_genomic.fna/target_genomes.txt --output GCF_020026915.1_ASM2002691v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:19,964] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:19,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:19,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:19,982] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:19,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:19,983] [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 panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	87.171	1348	1881	95	below_threshold
Flavobacterium chungbukense	strain=CS100	GCA_020805785.1	877464	877464	type	True	86.2961	1378	1881	95	below_threshold
Flavobacterium ginsenosidimutans	strain=THG 01	GCA_003254625.1	687844	687844	type	True	86.2262	1323	1881	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	85.88	1251	1881	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	85.6687	1201	1881	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	85.5932	1215	1881	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	85.5757	1197	1881	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	85.5566	1222	1881	95	below_threshold
Flavobacterium ustbae	strain=T13	GCA_003946915.1	2488790	2488790	type	True	85.4978	1232	1881	95	below_threshold
Flavobacterium anhuiense	strain=CGMCC 1.6859	GCA_900101855.1	459526	459526	suspected-type	True	85.2674	1235	1881	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	84.8356	1291	1881	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	84.7307	1335	1881	95	below_threshold
Flavobacterium fluviale	strain=HYN0086	GCA_003312915.1	2249356	2249356	type	True	84.7095	1211	1881	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	84.138	1172	1881	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	83.8663	1219	1881	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	83.4727	1078	1881	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	83.33	1050	1881	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.1828	1054	1881	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.3438	230	1881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:19,988] [INFO] DFAST Taxonomy check result was written to GCF_020026915.1_ASM2002691v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:19,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:19,989] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:19,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference/checkm_data
[2024-01-24 11:06:19,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:20,047] [INFO] Task started: CheckM
[2024-01-24 11:06:20,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020026915.1_ASM2002691v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020026915.1_ASM2002691v1_genomic.fna/checkm_input GCF_020026915.1_ASM2002691v1_genomic.fna/checkm_result
[2024-01-24 11:07:18,853] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:18,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:18,883] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:18,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:18,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020026915.1_ASM2002691v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:18,884] [INFO] Task started: Blastn
[2024-01-24 11:07:18,884] [INFO] Running command: blastn -query GCF_020026915.1_ASM2002691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b3320d4-e8f0-4878-a30f-2602c7b37434/dqc_reference/reference_markers_gtdb.fasta -out GCF_020026915.1_ASM2002691v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:19,844] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:19,849] [INFO] Selected 19 target genomes.
[2024-01-24 11:07:19,849] [INFO] Target genome list was writen to GCF_020026915.1_ASM2002691v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:19,863] [INFO] Task started: fastANI
[2024-01-24 11:07:19,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d9f934-83eb-4463-8612-2935451c634c/GCF_020026915.1_ASM2002691v1_genomic.fna.gz --refList GCF_020026915.1_ASM2002691v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020026915.1_ASM2002691v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:43,794] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:43,834] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:07:43,835] [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_902167265.1	s__Flavobacterium anhuiense_B	87.6084	1402	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	86.4588	1419	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	86.2351	1322	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744675.1	s__Flavobacterium sp017744675	86.1705	1225	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	85.9179	1286	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
GCF_002303885.1	s__Flavobacterium sp002303885	85.8948	1271	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013388355.1	s__Flavobacterium sp013388355	85.7799	915	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	85.6687	1201	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254545.1	s__Flavobacterium tistrianum	85.5743	1197	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	85.5729	1220	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003946915.1	s__Flavobacterium sp003946915	85.5159	1230	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151235.1	s__Flavobacterium anhuiense_A	85.4504	1233	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826975.1	s__Flavobacterium sp009826975	85.34	1245	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312915.1	s__Flavobacterium sp003312915	84.7095	1211	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352115.1	s__Flavobacterium sp017352115	84.1462	1171	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352915.1	s__Flavobacterium zhairuonense	83.4748	1078	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018383905.1	s__Flavobacterium branchiicola	83.4369	1043	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	83.3377	1049	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614725.1	s__Flavobacterium ajazii	82.2403	919	1881	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:43,837] [INFO] GTDB search result was written to GCF_020026915.1_ASM2002691v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:43,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:43,846] [INFO] DFAST_QC result json was written to GCF_020026915.1_ASM2002691v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:43,847] [INFO] DFAST_QC completed!
[2024-01-24 11:07:43,847] [INFO] Total running time: 0h2m9s