[2024-01-24 11:43:53,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference
[2024-01-24 11:43:54,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,511] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ebb779f-47fd-46b8-aa48-e75e92f28827/GCF_003031005.1_ASM303100v1_genomic.fna.gz | prodigal -d GCF_003031005.1_ASM303100v1_genomic.fna/cds.fna -a GCF_003031005.1_ASM303100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:17,418] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:17,418] [INFO] Task started: HMMsearch
[2024-01-24 11:44:17,418] [INFO] Running command: hmmsearch --tblout GCF_003031005.1_ASM303100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference/reference_markers.hmm GCF_003031005.1_ASM303100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:17,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:17,703] [INFO] Found 6/6 markers.
[2024-01-24 11:44:17,763] [INFO] Query marker FASTA was written to GCF_003031005.1_ASM303100v1_genomic.fna/markers.fasta
[2024-01-24 11:44:17,763] [INFO] Task started: Blastn
[2024-01-24 11:44:17,764] [INFO] Running command: blastn -query GCF_003031005.1_ASM303100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference/reference_markers.fasta -out GCF_003031005.1_ASM303100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:18,734] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:18,738] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:18,738] [INFO] Target genome list was writen to GCF_003031005.1_ASM303100v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:18,743] [INFO] Task started: fastANI
[2024-01-24 11:44:18,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebb779f-47fd-46b8-aa48-e75e92f28827/GCF_003031005.1_ASM303100v1_genomic.fna.gz --refList GCF_003031005.1_ASM303100v1_genomic.fna/target_genomes.txt --output GCF_003031005.1_ASM303100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:43,435] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:43,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:43,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:43,448] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:43,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:43,449] [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
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	100.0	2250	2251	95	conclusive
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	99.9576	2242	2251	95	conclusive
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	89.4166	1716	2251	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.4122	1708	2251	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	89.2617	1683	2251	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	89.2606	1696	2251	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.9583	1667	2251	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	88.9441	1672	2251	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.1802	1634	2251	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.9941	1567	2251	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	87.7774	1596	2251	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.1914	1260	2251	95	below_threshold
Pseudomonas fuscovaginae	strain=LMG 2158	GCA_900108595.1	50340	50340	suspected-type	True	82.3788	1119	2251	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.6041	824	2251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:43,450] [INFO] DFAST Taxonomy check result was written to GCF_003031005.1_ASM303100v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:43,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:43,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:43,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference/checkm_data
[2024-01-24 11:44:43,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:43,512] [INFO] Task started: CheckM
[2024-01-24 11:44:43,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003031005.1_ASM303100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003031005.1_ASM303100v1_genomic.fna/checkm_input GCF_003031005.1_ASM303100v1_genomic.fna/checkm_result
[2024-01-24 11:45:50,643] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:50,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:50,664] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:50,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:50,664] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003031005.1_ASM303100v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:50,664] [INFO] Task started: Blastn
[2024-01-24 11:45:50,665] [INFO] Running command: blastn -query GCF_003031005.1_ASM303100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg442ff288-dda9-42e2-b2a8-f7ba46a6e304/dqc_reference/reference_markers_gtdb.fasta -out GCF_003031005.1_ASM303100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:52,429] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:52,432] [INFO] Selected 16 target genomes.
[2024-01-24 11:45:52,432] [INFO] Target genome list was writen to GCF_003031005.1_ASM303100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:52,442] [INFO] Task started: fastANI
[2024-01-24 11:45:52,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebb779f-47fd-46b8-aa48-e75e92f28827/GCF_003031005.1_ASM303100v1_genomic.fna.gz --refList GCF_003031005.1_ASM303100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003031005.1_ASM303100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:20,517] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:20,530] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:20,530] [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_002813455.1	s__Pseudomonas_E baetica	99.9576	2243	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	95.55	0.93	0.86	4	conclusive
GCF_014472415.1	s__Pseudomonas_E sp014472415	91.0805	1627	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018326005.1	s__Pseudomonas_E sp002901475	89.9692	1722	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.45	98.45	0.94	0.94	2	-
GCF_016651305.1	s__Pseudomonas_E sp016651305	89.8209	1759	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011755.1	s__Pseudomonas_E sp004011755	89.5009	1713	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_900187605.1	s__Pseudomonas_E sp900187605	89.4173	1668	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	98.53	0.93	0.93	4	-
GCF_014268445.2	s__Pseudomonas_E sp900187515	89.4118	1719	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	89.3603	1678	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902497745.1	s__Pseudomonas_E fluorescens_BM	89.3272	1699	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938625.1	s__Pseudomonas_E fluorescens_BD	89.3005	1687	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013433315.1	s__Pseudomonas_E crudilactis	89.2638	1682	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.37	0.96	0.95	4	-
GCF_004124275.1	s__Pseudomonas_E sp004124275	89.1613	1672	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009764645.1	s__Pseudomonas_E sp009764645	89.0706	1519	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016650635.1	s__Pseudomonas_E sp016650635	89.0372	1721	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
GCF_012986595.1	s__Pseudomonas_E koreensis	88.9616	1666	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	-
GCF_013386115.1	s__Pseudomonas_E gingeri_B	83.1008	1189	2251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	98.43	0.94	0.92	9	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:20,531] [INFO] GTDB search result was written to GCF_003031005.1_ASM303100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:20,532] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:20,536] [INFO] DFAST_QC result json was written to GCF_003031005.1_ASM303100v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:20,536] [INFO] DFAST_QC completed!
[2024-01-24 11:46:20,536] [INFO] Total running time: 0h2m27s