[2023-06-30 12:00:10,694] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:00:10,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:00:10,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference
[2023-06-30 12:00:11,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:00:11,938] [INFO] Task started: Prodigal
[2023-06-30 12:00:11,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg831598bb-b447-42ae-9c0b-df4dbed89d64/GCA_008015405.1_ASM801540v1_genomic.fna.gz | prodigal -d GCA_008015405.1_ASM801540v1_genomic.fna/cds.fna -a GCA_008015405.1_ASM801540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:00:15,864] [INFO] Task succeeded: Prodigal
[2023-06-30 12:00:15,865] [INFO] Task started: HMMsearch
[2023-06-30 12:00:15,865] [INFO] Running command: hmmsearch --tblout GCA_008015405.1_ASM801540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference/reference_markers.hmm GCA_008015405.1_ASM801540v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:00:16,051] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:00:16,053] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg831598bb-b447-42ae-9c0b-df4dbed89d64/GCA_008015405.1_ASM801540v1_genomic.fna.gz]
[2023-06-30 12:00:16,074] [INFO] Query marker FASTA was written to GCA_008015405.1_ASM801540v1_genomic.fna/markers.fasta
[2023-06-30 12:00:16,074] [INFO] Task started: Blastn
[2023-06-30 12:00:16,074] [INFO] Running command: blastn -query GCA_008015405.1_ASM801540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference/reference_markers.fasta -out GCA_008015405.1_ASM801540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:16,703] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:16,710] [INFO] Selected 15 target genomes.
[2023-06-30 12:00:16,711] [INFO] Target genome list was writen to GCA_008015405.1_ASM801540v1_genomic.fna/target_genomes.txt
[2023-06-30 12:00:16,716] [INFO] Task started: fastANI
[2023-06-30 12:00:16,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg831598bb-b447-42ae-9c0b-df4dbed89d64/GCA_008015405.1_ASM801540v1_genomic.fna.gz --refList GCA_008015405.1_ASM801540v1_genomic.fna/target_genomes.txt --output GCA_008015405.1_ASM801540v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:00:28,163] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:28,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:00:28,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:00:28,177] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:00:28,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:00:28,177] [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 alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	88.3105	263	443	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	88.2425	258	443	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	83.3082	226	443	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.8214	203	443	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	82.5632	210	443	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	82.1371	199	443	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	81.8356	200	443	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	81.797	207	443	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	81.6058	191	443	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	81.4352	196	443	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	81.2257	191	443	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	81.1168	228	443	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	81.0844	229	443	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	80.6904	191	443	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	80.6345	179	443	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:00:28,179] [INFO] DFAST Taxonomy check result was written to GCA_008015405.1_ASM801540v1_genomic.fna/tc_result.tsv
[2023-06-30 12:00:28,180] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:00:28,180] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:00:28,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference/checkm_data
[2023-06-30 12:00:28,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:00:28,204] [INFO] Task started: CheckM
[2023-06-30 12:00:28,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008015405.1_ASM801540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008015405.1_ASM801540v1_genomic.fna/checkm_input GCA_008015405.1_ASM801540v1_genomic.fna/checkm_result
[2023-06-30 12:00:47,193] [INFO] Task succeeded: CheckM
[2023-06-30 12:00:47,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:00:47,220] [INFO] ===== Completeness check finished =====
[2023-06-30 12:00:47,221] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:00:47,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008015405.1_ASM801540v1_genomic.fna/markers.fasta)
[2023-06-30 12:00:47,222] [INFO] Task started: Blastn
[2023-06-30 12:00:47,222] [INFO] Running command: blastn -query GCA_008015405.1_ASM801540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee175533-4206-437d-b680-fea0b6cd0474/dqc_reference/reference_markers_gtdb.fasta -out GCA_008015405.1_ASM801540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:00:47,993] [INFO] Task succeeded: Blastn
[2023-06-30 12:00:47,998] [INFO] Selected 14 target genomes.
[2023-06-30 12:00:47,998] [INFO] Target genome list was writen to GCA_008015405.1_ASM801540v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:00:48,007] [INFO] Task started: fastANI
[2023-06-30 12:00:48,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg831598bb-b447-42ae-9c0b-df4dbed89d64/GCA_008015405.1_ASM801540v1_genomic.fna.gz --refList GCA_008015405.1_ASM801540v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008015405.1_ASM801540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:00:58,366] [INFO] Task succeeded: fastANI
[2023-06-30 12:00:58,383] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 12:00:58,383] [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_000467105.1	s__Pseudomonas_E alcaligenes	88.2954	257	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	86.4265	245	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	86.0896	241	443	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_000761545.1	s__Pseudomonas_E sp000761545	85.2791	236	443	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_014851865.1	s__Pseudomonas_E sp014851865	84.0484	230	443	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_900104265.1	s__Pseudomonas_E guguanensis	82.6004	209	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_002304225.1	s__Pseudomonas_E sp002304225	82.3572	193	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
GCF_000418555.1	s__Pseudomonas_E sp000418555	82.2051	192	443	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_009932725.1	s__Pseudomonas_E sp009932725	82.1371	199	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	81.9009	200	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_014207935.1	s__Pseudomonas_E fluvialis_A	81.8276	194	443	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_008807375.1	s__Pseudomonas_F lalkuanensis	81.0363	204	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949385.2	s__Pseudomonas_F sp000949385	80.6481	208	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	80.3827	202	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-30 12:00:58,385] [INFO] GTDB search result was written to GCA_008015405.1_ASM801540v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:00:58,386] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:00:58,391] [INFO] DFAST_QC result json was written to GCA_008015405.1_ASM801540v1_genomic.fna/dqc_result.json
[2023-06-30 12:00:58,392] [INFO] DFAST_QC completed!
[2023-06-30 12:00:58,392] [INFO] Total running time: 0h0m48s