[2024-01-24 13:21:10,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference
[2024-01-24 13:21:12,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,347] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,348] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b588b11-80ac-4d7b-b03d-6547e8e9cf39/GCF_009909155.2_ASM990915v2_genomic.fna.gz | prodigal -d GCF_009909155.2_ASM990915v2_genomic.fna/cds.fna -a GCF_009909155.2_ASM990915v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:27,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:27,836] [INFO] Task started: HMMsearch
[2024-01-24 13:21:27,837] [INFO] Running command: hmmsearch --tblout GCF_009909155.2_ASM990915v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference/reference_markers.hmm GCF_009909155.2_ASM990915v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:28,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:28,142] [INFO] Found 6/6 markers.
[2024-01-24 13:21:28,179] [INFO] Query marker FASTA was written to GCF_009909155.2_ASM990915v2_genomic.fna/markers.fasta
[2024-01-24 13:21:28,180] [INFO] Task started: Blastn
[2024-01-24 13:21:28,180] [INFO] Running command: blastn -query GCF_009909155.2_ASM990915v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference/reference_markers.fasta -out GCF_009909155.2_ASM990915v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:28,895] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:28,898] [INFO] Selected 14 target genomes.
[2024-01-24 13:21:28,899] [INFO] Target genome list was writen to GCF_009909155.2_ASM990915v2_genomic.fna/target_genomes.txt
[2024-01-24 13:21:28,907] [INFO] Task started: fastANI
[2024-01-24 13:21:28,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b588b11-80ac-4d7b-b03d-6547e8e9cf39/GCF_009909155.2_ASM990915v2_genomic.fna.gz --refList GCF_009909155.2_ASM990915v2_genomic.fna/target_genomes.txt --output GCF_009909155.2_ASM990915v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:42,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:42,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:42,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:42,686] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:42,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:42,686] [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 undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	100.0	1378	1383	95	conclusive
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	90.1266	1082	1383	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	86.5612	908	1383	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	84.2699	903	1383	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	84.0462	793	1383	95	below_threshold
Flavobacterium flevense	strain=DSM 1076	GCA_900142775.1	983	983	type	True	83.9487	873	1383	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	83.8016	862	1383	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	79.0365	458	1383	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	78.9434	432	1383	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.8755	452	1383	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.7951	428	1383	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.7797	465	1383	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.7223	445	1383	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.0148	146	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:42,689] [INFO] DFAST Taxonomy check result was written to GCF_009909155.2_ASM990915v2_genomic.fna/tc_result.tsv
[2024-01-24 13:21:42,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:42,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:42,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference/checkm_data
[2024-01-24 13:21:42,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:42,741] [INFO] Task started: CheckM
[2024-01-24 13:21:42,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009909155.2_ASM990915v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009909155.2_ASM990915v2_genomic.fna/checkm_input GCF_009909155.2_ASM990915v2_genomic.fna/checkm_result
[2024-01-24 13:22:29,631] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:29,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:29,656] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:29,657] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:29,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009909155.2_ASM990915v2_genomic.fna/markers.fasta)
[2024-01-24 13:22:29,658] [INFO] Task started: Blastn
[2024-01-24 13:22:29,658] [INFO] Running command: blastn -query GCF_009909155.2_ASM990915v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec9d4d9-3d9d-4546-9428-dc58bd821394/dqc_reference/reference_markers_gtdb.fasta -out GCF_009909155.2_ASM990915v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:30,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:30,817] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:30,817] [INFO] Target genome list was writen to GCF_009909155.2_ASM990915v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:30,833] [INFO] Task started: fastANI
[2024-01-24 13:22:30,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b588b11-80ac-4d7b-b03d-6547e8e9cf39/GCF_009909155.2_ASM990915v2_genomic.fna.gz --refList GCF_009909155.2_ASM990915v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009909155.2_ASM990915v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:41,636] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:41,654] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:41,655] [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_009909155.2	s__Flavobacterium undicola	100.0	1378	1383	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_004016525.1	s__Flavobacterium sufflavum	90.1026	1083	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	86.767	680	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857965.1	s__Flavobacterium commune	86.5553	908	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCF_014639535.1	s__Flavobacterium palustre	84.2483	905	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	84.0463	793	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142775.1	s__Flavobacterium flevense	83.9567	873	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425425.1	s__Flavobacterium daejeonense	82.1034	820	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	79.0182	483	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_002217395.1	s__Flavobacterium plurextorum	78.9538	431	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:41,656] [INFO] GTDB search result was written to GCF_009909155.2_ASM990915v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:41,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:41,663] [INFO] DFAST_QC result json was written to GCF_009909155.2_ASM990915v2_genomic.fna/dqc_result.json
[2024-01-24 13:22:41,663] [INFO] DFAST_QC completed!
[2024-01-24 13:22:41,663] [INFO] Total running time: 0h1m31s