[2024-01-24 13:49:54,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:54,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:54,958] [INFO] DQC Reference Directory: /var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference
[2024-01-24 13:49:56,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,102] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg46b8e06d-a244-4e5f-a594-b5908d7d2a94/GCF_019308285.1_ASM1930828v1_genomic.fna.gz | prodigal -d GCF_019308285.1_ASM1930828v1_genomic.fna/cds.fna -a GCF_019308285.1_ASM1930828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:13,367] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:13,367] [INFO] Task started: HMMsearch
[2024-01-24 13:50:13,367] [INFO] Running command: hmmsearch --tblout GCF_019308285.1_ASM1930828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference/reference_markers.hmm GCF_019308285.1_ASM1930828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:13,613] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:13,614] [INFO] Found 6/6 markers.
[2024-01-24 13:50:13,658] [INFO] Query marker FASTA was written to GCF_019308285.1_ASM1930828v1_genomic.fna/markers.fasta
[2024-01-24 13:50:13,658] [INFO] Task started: Blastn
[2024-01-24 13:50:13,658] [INFO] Running command: blastn -query GCF_019308285.1_ASM1930828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference/reference_markers.fasta -out GCF_019308285.1_ASM1930828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:14,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:14,292] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:14,293] [INFO] Target genome list was writen to GCF_019308285.1_ASM1930828v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:14,297] [INFO] Task started: fastANI
[2024-01-24 13:50:14,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg46b8e06d-a244-4e5f-a594-b5908d7d2a94/GCF_019308285.1_ASM1930828v1_genomic.fna.gz --refList GCF_019308285.1_ASM1930828v1_genomic.fna/target_genomes.txt --output GCF_019308285.1_ASM1930828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:33,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:33,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:33,089] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:33,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:33,090] [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 quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	100.0	2027	2034	95	conclusive
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	91.3962	1613	2034	95	below_threshold
Flavobacterium crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	90.0399	1591	2034	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	86.0087	1484	2034	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	85.5296	1194	2034	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	85.5163	1214	2034	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	85.3236	1226	2034	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	85.301	1266	2034	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	84.3114	1262	2034	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	84.3075	1276	2034	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	84.2635	1272	2034	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.4214	1088	2034	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	83.3863	1054	2034	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.1648	1181	2034	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	76.7198	244	2034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,091] [INFO] DFAST Taxonomy check result was written to GCF_019308285.1_ASM1930828v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:33,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:33,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:33,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference/checkm_data
[2024-01-24 13:50:33,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:33,151] [INFO] Task started: CheckM
[2024-01-24 13:50:33,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019308285.1_ASM1930828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019308285.1_ASM1930828v1_genomic.fna/checkm_input GCF_019308285.1_ASM1930828v1_genomic.fna/checkm_result
[2024-01-24 13:51:22,177] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:22,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:22,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:22,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:22,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019308285.1_ASM1930828v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:22,192] [INFO] Task started: Blastn
[2024-01-24 13:51:22,192] [INFO] Running command: blastn -query GCF_019308285.1_ASM1930828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3bbff40-4b25-4c8d-816e-d685e462ae04/dqc_reference/reference_markers_gtdb.fasta -out GCF_019308285.1_ASM1930828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:23,121] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:23,123] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:23,124] [INFO] Target genome list was writen to GCF_019308285.1_ASM1930828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:23,132] [INFO] Task started: fastANI
[2024-01-24 13:51:23,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg46b8e06d-a244-4e5f-a594-b5908d7d2a94/GCF_019308285.1_ASM1930828v1_genomic.fna.gz --refList GCF_019308285.1_ASM1930828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019308285.1_ASM1930828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:41,169] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:41,177] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:41,178] [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_013393195.1	s__Flavobacterium collinsii_A	99.7183	1897	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112575.1	s__Flavobacterium phragmitis	91.4067	1612	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122385.1	s__Flavobacterium crocinum	90.0399	1591	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	86.5146	1382	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	85.729	1518	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_013388355.1	s__Flavobacterium sp013388355	85.5831	959	2034	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	85.5389	1193	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002303885.1	s__Flavobacterium sp002303885	85.4431	1276	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735615.1	s__Flavobacterium sp016735615	85.4377	1265	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	85.4098	1351	2034	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	85.3237	1226	2034	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	85.1858	1244	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	84.3114	1262	2034	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_000425445.1	s__Flavobacterium denitrificans	83.4014	1053	2034	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 13:51:41,179] [INFO] GTDB search result was written to GCF_019308285.1_ASM1930828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:41,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:41,182] [INFO] DFAST_QC result json was written to GCF_019308285.1_ASM1930828v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:41,182] [INFO] DFAST_QC completed!
[2024-01-24 13:51:41,182] [INFO] Total running time: 0h1m46s