[2024-01-24 11:12:27,796] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference
[2024-01-24 11:12:29,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,207] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbb849b0-7c68-4b65-ad4a-96d0958ee194/GCF_003315595.1_ASM331559v1_genomic.fna.gz | prodigal -d GCF_003315595.1_ASM331559v1_genomic.fna/cds.fna -a GCF_003315595.1_ASM331559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:55,189] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:55,189] [INFO] Task started: HMMsearch
[2024-01-24 11:12:55,189] [INFO] Running command: hmmsearch --tblout GCF_003315595.1_ASM331559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference/reference_markers.hmm GCF_003315595.1_ASM331559v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:55,614] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:55,615] [INFO] Found 6/6 markers.
[2024-01-24 11:12:55,677] [INFO] Query marker FASTA was written to GCF_003315595.1_ASM331559v1_genomic.fna/markers.fasta
[2024-01-24 11:12:55,678] [INFO] Task started: Blastn
[2024-01-24 11:12:55,678] [INFO] Running command: blastn -query GCF_003315595.1_ASM331559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference/reference_markers.fasta -out GCF_003315595.1_ASM331559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:56,338] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:56,342] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:56,343] [INFO] Target genome list was writen to GCF_003315595.1_ASM331559v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:56,348] [INFO] Task started: fastANI
[2024-01-24 11:12:56,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbb849b0-7c68-4b65-ad4a-96d0958ee194/GCF_003315595.1_ASM331559v1_genomic.fna.gz --refList GCF_003315595.1_ASM331559v1_genomic.fna/target_genomes.txt --output GCF_003315595.1_ASM331559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:16,138] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:16,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:16,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:16,150] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:16,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:16,151] [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
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	100.0	2191	2194	95	conclusive
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	83.1658	1027	2194	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	83.1359	1156	2194	95	below_threshold
Pedobacter zeae	strain=CGMCC 1.15287	GCA_014641575.1	1737356	1737356	type	True	83.0689	1155	2194	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	83.0642	1149	2194	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	82.9939	1221	2194	95	below_threshold
Pedobacter zeae	strain=DSM 100774	GCA_014196715.1	1737356	1737356	type	True	82.9789	1152	2194	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	82.978	1184	2194	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	82.7326	1196	2194	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	82.5248	1073	2194	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.771	1056	2194	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.8038	748	2194	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	78.7532	544	2194	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.5835	112	2194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:16,152] [INFO] DFAST Taxonomy check result was written to GCF_003315595.1_ASM331559v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:16,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:16,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:16,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference/checkm_data
[2024-01-24 11:13:16,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:16,221] [INFO] Task started: CheckM
[2024-01-24 11:13:16,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315595.1_ASM331559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315595.1_ASM331559v1_genomic.fna/checkm_input GCF_003315595.1_ASM331559v1_genomic.fna/checkm_result
[2024-01-24 11:14:25,523] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:25,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:25,548] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:25,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:25,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315595.1_ASM331559v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:25,549] [INFO] Task started: Blastn
[2024-01-24 11:14:25,550] [INFO] Running command: blastn -query GCF_003315595.1_ASM331559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacfa715f-ccd5-4604-9d84-0a33dd81858a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315595.1_ASM331559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:26,366] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:26,371] [INFO] Selected 11 target genomes.
[2024-01-24 11:14:26,371] [INFO] Target genome list was writen to GCF_003315595.1_ASM331559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:26,378] [INFO] Task started: fastANI
[2024-01-24 11:14:26,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbb849b0-7c68-4b65-ad4a-96d0958ee194/GCF_003315595.1_ASM331559v1_genomic.fna.gz --refList GCF_003315595.1_ASM331559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315595.1_ASM331559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:42,612] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:42,626] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:42,626] [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_003315595.1	s__Pedobacter miscanthi	100.0	2191	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002432345.1	s__Pedobacter sp002432345	87.9273	1440	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	85.133	1443	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395225.1	s__Pedobacter roseus	84.994	1444	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745075.1	s__Pedobacter sp017745075	83.4804	1158	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994015.1	s__Pedobacter terrae_A	83.1353	1195	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664035.1	s__Pedobacter alluvionis	83.129	1157	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014692875.1	s__Pedobacter sp011759615	83.02	1169	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	83.0018	1219	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196715.1	s__Pedobacter zeae	82.9884	1152	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100705.1	s__Pedobacter terrae	82.5463	1069	2194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:42,628] [INFO] GTDB search result was written to GCF_003315595.1_ASM331559v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:42,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:42,633] [INFO] DFAST_QC result json was written to GCF_003315595.1_ASM331559v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:42,633] [INFO] DFAST_QC completed!
[2024-01-24 11:14:42,634] [INFO] Total running time: 0h2m15s