[2024-01-24 12:23:34,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:34,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:34,298] [INFO] DQC Reference Directory: /var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference
[2024-01-24 12:23:35,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:35,669] [INFO] Task started: Prodigal
[2024-01-24 12:23:35,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg5598b452-3bc8-45bc-8889-8539ca707e38/GCF_007830055.1_ASM783005v1_genomic.fna.gz | prodigal -d GCF_007830055.1_ASM783005v1_genomic.fna/cds.fna -a GCF_007830055.1_ASM783005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:01,145] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:01,145] [INFO] Task started: HMMsearch
[2024-01-24 12:24:01,145] [INFO] Running command: hmmsearch --tblout GCF_007830055.1_ASM783005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference/reference_markers.hmm GCF_007830055.1_ASM783005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:01,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:01,383] [INFO] Found 6/6 markers.
[2024-01-24 12:24:01,424] [INFO] Query marker FASTA was written to GCF_007830055.1_ASM783005v1_genomic.fna/markers.fasta
[2024-01-24 12:24:01,425] [INFO] Task started: Blastn
[2024-01-24 12:24:01,425] [INFO] Running command: blastn -query GCF_007830055.1_ASM783005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference/reference_markers.fasta -out GCF_007830055.1_ASM783005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:01,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:01,995] [INFO] Selected 24 target genomes.
[2024-01-24 12:24:01,995] [INFO] Target genome list was writen to GCF_007830055.1_ASM783005v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:02,003] [INFO] Task started: fastANI
[2024-01-24 12:24:02,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg5598b452-3bc8-45bc-8889-8539ca707e38/GCF_007830055.1_ASM783005v1_genomic.fna.gz --refList GCF_007830055.1_ASM783005v1_genomic.fna/target_genomes.txt --output GCF_007830055.1_ASM783005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:25,503] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:25,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:25,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:25,520] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:25,520] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:25,520] [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
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	100.0	1643	1645	95	conclusive
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	84.5482	1175	1645	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.196	82	1645	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	77.0457	90	1645	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	76.9706	78	1645	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.7545	121	1645	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.5941	117	1645	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.5238	96	1645	95	below_threshold
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	76.4597	61	1645	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.2975	93	1645	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.2728	121	1645	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.2474	111	1645	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.22	91	1645	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.1896	74	1645	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.1741	59	1645	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.1236	117	1645	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	76.0953	100	1645	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.0796	111	1645	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.017	112	1645	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.014	69	1645	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.9366	56	1645	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.79	109	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:25,522] [INFO] DFAST Taxonomy check result was written to GCF_007830055.1_ASM783005v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:25,522] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:25,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:25,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference/checkm_data
[2024-01-24 12:24:25,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:25,568] [INFO] Task started: CheckM
[2024-01-24 12:24:25,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830055.1_ASM783005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830055.1_ASM783005v1_genomic.fna/checkm_input GCF_007830055.1_ASM783005v1_genomic.fna/checkm_result
[2024-01-24 12:25:33,488] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:33,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:33,513] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:33,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:33,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830055.1_ASM783005v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:33,513] [INFO] Task started: Blastn
[2024-01-24 12:25:33,513] [INFO] Running command: blastn -query GCF_007830055.1_ASM783005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd93fd9-b298-47ed-9bf4-bbcf1c6055d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830055.1_ASM783005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:34,247] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:34,250] [INFO] Selected 11 target genomes.
[2024-01-24 12:25:34,250] [INFO] Target genome list was writen to GCF_007830055.1_ASM783005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:34,259] [INFO] Task started: fastANI
[2024-01-24 12:25:34,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg5598b452-3bc8-45bc-8889-8539ca707e38/GCF_007830055.1_ASM783005v1_genomic.fna.gz --refList GCF_007830055.1_ASM783005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830055.1_ASM783005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:43,245] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:43,254] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:43,254] [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_007830055.1	s__Lacibacter cauensis	100.0	1644	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004118265.1	s__Lacibacter luteus	84.546	1175	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996555.1	s__Lacibacter sp009996555	82.5394	599	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014168535.1	s__Lacibacter sp014168535	80.6984	910	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337125.1	s__Lacibacter sp002337125	78.5464	565	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713085.1	s__Lacibacter sp016713085	78.3542	566	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336115.1	s__Lacibacter sp002336115	78.1771	414	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	99.94	99.94	0.95	0.95	2	-
GCF_007971225.1	s__Panacibacter ginsenosidivorans	76.2672	120	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787125.1	s__JJ008 sp016787125	76.2122	73	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455235.1	s__Ferruginibacter sp003455235	75.3167	51	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:43,257] [INFO] GTDB search result was written to GCF_007830055.1_ASM783005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:43,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:43,262] [INFO] DFAST_QC result json was written to GCF_007830055.1_ASM783005v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:43,262] [INFO] DFAST_QC completed!
[2024-01-24 12:25:43,262] [INFO] Total running time: 0h2m9s