[2024-01-24 12:40:07,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,102] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference
[2024-01-24 12:40:08,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,432] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg68bdbdcb-3746-40f1-95fd-4c47264abb16/GCF_004801935.1_ASM480193v1_genomic.fna.gz | prodigal -d GCF_004801935.1_ASM480193v1_genomic.fna/cds.fna -a GCF_004801935.1_ASM480193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:28,038] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:28,038] [INFO] Task started: HMMsearch
[2024-01-24 12:40:28,038] [INFO] Running command: hmmsearch --tblout GCF_004801935.1_ASM480193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference/reference_markers.hmm GCF_004801935.1_ASM480193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:28,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:28,306] [INFO] Found 6/6 markers.
[2024-01-24 12:40:28,357] [INFO] Query marker FASTA was written to GCF_004801935.1_ASM480193v1_genomic.fna/markers.fasta
[2024-01-24 12:40:28,357] [INFO] Task started: Blastn
[2024-01-24 12:40:28,357] [INFO] Running command: blastn -query GCF_004801935.1_ASM480193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference/reference_markers.fasta -out GCF_004801935.1_ASM480193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:29,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:29,305] [INFO] Selected 13 target genomes.
[2024-01-24 12:40:29,305] [INFO] Target genome list was writen to GCF_004801935.1_ASM480193v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:29,310] [INFO] Task started: fastANI
[2024-01-24 12:40:29,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg68bdbdcb-3746-40f1-95fd-4c47264abb16/GCF_004801935.1_ASM480193v1_genomic.fna.gz --refList GCF_004801935.1_ASM480193v1_genomic.fna/target_genomes.txt --output GCF_004801935.1_ASM480193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:51,110] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:51,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:51,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:51,122] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:40:51,122] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:40:51,123] [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 atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	100.0	2050	2051	95	inconclusive
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	96.541	1800	2051	95	inconclusive
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	96.321	1790	2051	95	inconclusive
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	96.0938	1726	2051	95	inconclusive
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	89.5031	1662	2051	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	88.6388	1660	2051	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.4923	1640	2051	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.4308	1623	2051	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.1189	1596	2051	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	87.6038	1582	2051	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.4912	1527	2051	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.1647	1233	2051	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.7937	841	2051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:51,124] [INFO] DFAST Taxonomy check result was written to GCF_004801935.1_ASM480193v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:51,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:51,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:51,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference/checkm_data
[2024-01-24 12:40:51,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:51,182] [INFO] Task started: CheckM
[2024-01-24 12:40:51,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801935.1_ASM480193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801935.1_ASM480193v1_genomic.fna/checkm_input GCF_004801935.1_ASM480193v1_genomic.fna/checkm_result
[2024-01-24 12:41:47,104] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:47,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:47,123] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:47,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:47,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801935.1_ASM480193v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:47,123] [INFO] Task started: Blastn
[2024-01-24 12:41:47,123] [INFO] Running command: blastn -query GCF_004801935.1_ASM480193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb6629ad-0729-43a6-a3af-5cb08c938b7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801935.1_ASM480193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:49,051] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:49,054] [INFO] Selected 8 target genomes.
[2024-01-24 12:41:49,054] [INFO] Target genome list was writen to GCF_004801935.1_ASM480193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:49,059] [INFO] Task started: fastANI
[2024-01-24 12:41:49,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg68bdbdcb-3746-40f1-95fd-4c47264abb16/GCF_004801935.1_ASM480193v1_genomic.fna.gz --refList GCF_004801935.1_ASM480193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801935.1_ASM480193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:07,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:07,074] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:07,074] [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_004801935.1	s__Pseudomonas_E atacamensis	100.0	2050	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	conclusive
GCF_001605965.1	s__Pseudomonas_E koreensis_C	95.4947	1810	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	-
GCF_000817895.1	s__Pseudomonas_E fluorescens_AO	94.4846	1733	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	92.7911	1681	2051	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_900105805.1	s__Pseudomonas_E moraviensis_A	92.6695	1777	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_900105485.1	s__Pseudomonas_E granadensis	88.6437	1659	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
GCF_900582195.1	s__Pseudomonas_E sp900582195	88.5353	1623	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.42	0.95	0.95	2	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	88.016	1592	2051	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:07,076] [INFO] GTDB search result was written to GCF_004801935.1_ASM480193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:07,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:07,079] [INFO] DFAST_QC result json was written to GCF_004801935.1_ASM480193v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:07,079] [INFO] DFAST_QC completed!
[2024-01-24 12:42:07,079] [INFO] Total running time: 0h1m60s