[2024-01-24 14:56:23,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference
[2024-01-24 14:56:26,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,560] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg67a43cd6-ec9e-4cdd-92df-c3b754496305/GCF_014642875.1_ASM1464287v1_genomic.fna.gz | prodigal -d GCF_014642875.1_ASM1464287v1_genomic.fna/cds.fna -a GCF_014642875.1_ASM1464287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:57:08,891] [INFO] Task succeeded: Prodigal
[2024-01-24 14:57:08,891] [INFO] Task started: HMMsearch
[2024-01-24 14:57:08,891] [INFO] Running command: hmmsearch --tblout GCF_014642875.1_ASM1464287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference/reference_markers.hmm GCF_014642875.1_ASM1464287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:57:09,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:57:09,350] [INFO] Found 6/6 markers.
[2024-01-24 14:57:09,409] [INFO] Query marker FASTA was written to GCF_014642875.1_ASM1464287v1_genomic.fna/markers.fasta
[2024-01-24 14:57:09,410] [INFO] Task started: Blastn
[2024-01-24 14:57:09,410] [INFO] Running command: blastn -query GCF_014642875.1_ASM1464287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference/reference_markers.fasta -out GCF_014642875.1_ASM1464287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:10,055] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:10,059] [INFO] Selected 24 target genomes.
[2024-01-24 14:57:10,060] [INFO] Target genome list was writen to GCF_014642875.1_ASM1464287v1_genomic.fna/target_genomes.txt
[2024-01-24 14:57:10,074] [INFO] Task started: fastANI
[2024-01-24 14:57:10,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a43cd6-ec9e-4cdd-92df-c3b754496305/GCF_014642875.1_ASM1464287v1_genomic.fna.gz --refList GCF_014642875.1_ASM1464287v1_genomic.fna/target_genomes.txt --output GCF_014642875.1_ASM1464287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:40,452] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:40,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:40,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:40,468] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:57:40,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:40,468] [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
Puia dinghuensis	strain=CGMCC 1.15448	GCA_014642875.1	1792502	1792502	type	True	100.0	2382	2383	95	conclusive
Dinghuibacter silviterrae	strain=DSM 100059	GCA_004366355.1	1539049	1539049	type	True	76.8001	133	2383	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.242	106	2383	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.1717	76	2383	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.1161	96	2383	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.0761	104	2383	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.0693	105	2383	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.062	105	2383	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.0243	63	2383	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	76.0034	117	2383	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	75.9924	120	2383	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.8824	104	2383	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	75.8784	79	2383	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.8673	98	2383	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	75.826	79	2383	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.6392	51	2383	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	75.4161	54	2383	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.4002	57	2383	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	75.001	58	2383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:40,470] [INFO] DFAST Taxonomy check result was written to GCF_014642875.1_ASM1464287v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:40,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:40,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:40,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference/checkm_data
[2024-01-24 14:57:40,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:40,541] [INFO] Task started: CheckM
[2024-01-24 14:57:40,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642875.1_ASM1464287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642875.1_ASM1464287v1_genomic.fna/checkm_input GCF_014642875.1_ASM1464287v1_genomic.fna/checkm_result
[2024-01-24 14:59:24,348] [INFO] Task succeeded: CheckM
[2024-01-24 14:59:24,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:59:24,371] [INFO] ===== Completeness check finished =====
[2024-01-24 14:59:24,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:59:24,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642875.1_ASM1464287v1_genomic.fna/markers.fasta)
[2024-01-24 14:59:24,372] [INFO] Task started: Blastn
[2024-01-24 14:59:24,373] [INFO] Running command: blastn -query GCF_014642875.1_ASM1464287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0670d812-31bc-4f55-8070-b77cb409e656/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642875.1_ASM1464287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:59:25,177] [INFO] Task succeeded: Blastn
[2024-01-24 14:59:25,181] [INFO] Selected 12 target genomes.
[2024-01-24 14:59:25,181] [INFO] Target genome list was writen to GCF_014642875.1_ASM1464287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:59:25,195] [INFO] Task started: fastANI
[2024-01-24 14:59:25,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a43cd6-ec9e-4cdd-92df-c3b754496305/GCF_014642875.1_ASM1464287v1_genomic.fna.gz --refList GCF_014642875.1_ASM1464287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642875.1_ASM1464287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:59:39,577] [INFO] Task succeeded: fastANI
[2024-01-24 14:59:39,599] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:59:39,600] [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_014642875.1	s__Puia dinghuensis	100.0	2382	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018267545.1	s__Puia sp018267545	77.9288	459	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267585.1	s__Puia sp018267585	77.8171	439	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167015.1	s__Puia sp003167015	77.5381	377	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898505.1	s__Puia sp001898505	77.4173	402	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017307755.1	s__Puia sp017307755	77.3627	396	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654595.1	s__Puia sp015654595	77.2864	359	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655015.1	s__Puia sp015655015	77.0569	289	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	76.2559	105	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004337505.1	s__Flaviaesturariibacter flavus	76.1717	76	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721725.1	s__Ferruginibacter sp016721725	76.0285	58	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.24	99.24	0.96	0.96	2	-
GCF_007992715.1	s__Chitinophaga cymbidii	75.6213	76	2383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:59:39,602] [INFO] GTDB search result was written to GCF_014642875.1_ASM1464287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:59:39,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:59:39,609] [INFO] DFAST_QC result json was written to GCF_014642875.1_ASM1464287v1_genomic.fna/dqc_result.json
[2024-01-24 14:59:39,610] [INFO] DFAST_QC completed!
[2024-01-24 14:59:39,610] [INFO] Total running time: 0h3m16s