[2024-01-24 15:18:27,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,493] [INFO] DQC Reference Directory: /var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference
[2024-01-24 15:18:28,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,993] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,993] [INFO] Running command: gunzip -c /var/lib/cwl/stg7273ec30-341f-44a7-b694-59900a23f6cb/GCF_004335085.1_ASM433508v1_genomic.fna.gz | prodigal -d GCF_004335085.1_ASM433508v1_genomic.fna/cds.fna -a GCF_004335085.1_ASM433508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:47,183] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:47,183] [INFO] Task started: HMMsearch
[2024-01-24 15:18:47,183] [INFO] Running command: hmmsearch --tblout GCF_004335085.1_ASM433508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference/reference_markers.hmm GCF_004335085.1_ASM433508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:47,545] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:47,547] [INFO] Found 6/6 markers.
[2024-01-24 15:18:47,596] [INFO] Query marker FASTA was written to GCF_004335085.1_ASM433508v1_genomic.fna/markers.fasta
[2024-01-24 15:18:47,596] [INFO] Task started: Blastn
[2024-01-24 15:18:47,596] [INFO] Running command: blastn -query GCF_004335085.1_ASM433508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference/reference_markers.fasta -out GCF_004335085.1_ASM433508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:48,248] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:48,251] [INFO] Selected 18 target genomes.
[2024-01-24 15:18:48,251] [INFO] Target genome list was writen to GCF_004335085.1_ASM433508v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:48,258] [INFO] Task started: fastANI
[2024-01-24 15:18:48,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg7273ec30-341f-44a7-b694-59900a23f6cb/GCF_004335085.1_ASM433508v1_genomic.fna.gz --refList GCF_004335085.1_ASM433508v1_genomic.fna/target_genomes.txt --output GCF_004335085.1_ASM433508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:07,364] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:07,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:07,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:07,380] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:07,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:07,381] [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 nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	100.0	1714	1717	95	conclusive
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	80.2992	685	1717	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	80.2864	635	1717	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	80.212	642	1717	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	80.1291	647	1717	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	80.0963	630	1717	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	80.0746	671	1717	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	80.0654	627	1717	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	80.0261	635	1717	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	79.981	637	1717	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	79.9487	621	1717	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	79.7314	644	1717	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	79.7146	625	1717	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.6628	603	1717	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	79.4733	623	1717	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.9613	84	1717	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.6625	64	1717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:07,382] [INFO] DFAST Taxonomy check result was written to GCF_004335085.1_ASM433508v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:07,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:07,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:07,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference/checkm_data
[2024-01-24 15:19:07,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:07,434] [INFO] Task started: CheckM
[2024-01-24 15:19:07,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004335085.1_ASM433508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004335085.1_ASM433508v1_genomic.fna/checkm_input GCF_004335085.1_ASM433508v1_genomic.fna/checkm_result
[2024-01-24 15:19:57,662] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:57,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:57,691] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:57,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:57,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004335085.1_ASM433508v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:57,692] [INFO] Task started: Blastn
[2024-01-24 15:19:57,692] [INFO] Running command: blastn -query GCF_004335085.1_ASM433508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f34091-9b21-4817-b09c-44b4a132c3a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004335085.1_ASM433508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:58,563] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:58,568] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:58,568] [INFO] Target genome list was writen to GCF_004335085.1_ASM433508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:58,579] [INFO] Task started: fastANI
[2024-01-24 15:19:58,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg7273ec30-341f-44a7-b694-59900a23f6cb/GCF_004335085.1_ASM433508v1_genomic.fna.gz --refList GCF_004335085.1_ASM433508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004335085.1_ASM433508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:18,350] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:18,369] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:18,369] [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_004335085.1	s__Pedobacter nototheniae	100.0	1714	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	conclusive
GCF_003387415.1	s__Pedobacter sp003387415	80.3472	646	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306625.1	s__Pedobacter sp014306625	80.3079	684	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339865.1	s__Pedobacter chinensis	80.2995	634	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173575.1	s__Pedobacter paludis	80.2368	688	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	80.2302	640	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	80.1475	634	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331735.1	s__Pedobacter sp004331735	80.1225	649	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	80.0796	651	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708285.2	s__Pedobacter borealis	80.0795	632	1717	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	79.9745	689	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205835.1	s__Pedobacter sp014205835	79.934	657	1717	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	79.9276	638	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303555.1	s__Pedobacter sp003852395	79.7407	627	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.47	99.47	0.90	0.90	2	-
GCF_003315595.1	s__Pedobacter miscanthi	79.7314	644	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100705.1	s__Pedobacter terrae	79.71	626	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903166585.1	s__Pedobacter sp903166585	79.6672	603	1717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688475.1	s__Pedobacter sp003688475	79.5625	533	1717	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 15:20:18,371] [INFO] GTDB search result was written to GCF_004335085.1_ASM433508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:18,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:18,376] [INFO] DFAST_QC result json was written to GCF_004335085.1_ASM433508v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:18,376] [INFO] DFAST_QC completed!
[2024-01-24 15:20:18,376] [INFO] Total running time: 0h1m51s