[2024-01-24 10:57:13,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference
[2024-01-24 10:57:14,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,555] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg59bb78d4-1226-4a68-854f-90ab8f50a770/GCF_024296925.1_ASM2429692v1_genomic.fna.gz | prodigal -d GCF_024296925.1_ASM2429692v1_genomic.fna/cds.fna -a GCF_024296925.1_ASM2429692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:42,782] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:42,782] [INFO] Task started: HMMsearch
[2024-01-24 10:57:42,782] [INFO] Running command: hmmsearch --tblout GCF_024296925.1_ASM2429692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference/reference_markers.hmm GCF_024296925.1_ASM2429692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:43,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:43,168] [INFO] Found 6/6 markers.
[2024-01-24 10:57:43,244] [INFO] Query marker FASTA was written to GCF_024296925.1_ASM2429692v1_genomic.fna/markers.fasta
[2024-01-24 10:57:43,245] [INFO] Task started: Blastn
[2024-01-24 10:57:43,245] [INFO] Running command: blastn -query GCF_024296925.1_ASM2429692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference/reference_markers.fasta -out GCF_024296925.1_ASM2429692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:44,290] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:44,293] [INFO] Selected 18 target genomes.
[2024-01-24 10:57:44,294] [INFO] Target genome list was writen to GCF_024296925.1_ASM2429692v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:44,300] [INFO] Task started: fastANI
[2024-01-24 10:57:44,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg59bb78d4-1226-4a68-854f-90ab8f50a770/GCF_024296925.1_ASM2429692v1_genomic.fna.gz --refList GCF_024296925.1_ASM2429692v1_genomic.fna/target_genomes.txt --output GCF_024296925.1_ASM2429692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:17,222] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:17,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:17,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:17,240] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:17,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:17,241] [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 mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	88.0808	1693	2442	95	below_threshold
Pseudomonas mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	88.0808	1728	2442	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	88.0795	1667	2442	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	87.9529	1607	2442	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	87.8891	1588	2442	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	87.8863	1591	2442	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	86.7275	1538	2442	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	86.72	1524	2442	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	86.6524	1532	2442	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	86.6427	1481	2442	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	86.5921	1485	2442	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	86.5812	1530	2442	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	86.5207	1521	2442	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	86.5057	1529	2442	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.2884	1645	2442	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.1396	1599	2442	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.6543	1651	2442	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.9417	1350	2442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,242] [INFO] DFAST Taxonomy check result was written to GCF_024296925.1_ASM2429692v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:17,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:17,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:17,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference/checkm_data
[2024-01-24 10:58:17,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:17,312] [INFO] Task started: CheckM
[2024-01-24 10:58:17,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024296925.1_ASM2429692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024296925.1_ASM2429692v1_genomic.fna/checkm_input GCF_024296925.1_ASM2429692v1_genomic.fna/checkm_result
[2024-01-24 10:59:37,904] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:37,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:37,926] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:37,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:37,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024296925.1_ASM2429692v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:37,927] [INFO] Task started: Blastn
[2024-01-24 10:59:37,928] [INFO] Running command: blastn -query GCF_024296925.1_ASM2429692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89267cf8-353b-4be8-aba1-9c42ded1a818/dqc_reference/reference_markers_gtdb.fasta -out GCF_024296925.1_ASM2429692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:39,586] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:39,589] [INFO] Selected 10 target genomes.
[2024-01-24 10:59:39,590] [INFO] Target genome list was writen to GCF_024296925.1_ASM2429692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:39,597] [INFO] Task started: fastANI
[2024-01-24 10:59:39,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg59bb78d4-1226-4a68-854f-90ab8f50a770/GCF_024296925.1_ASM2429692v1_genomic.fna.gz --refList GCF_024296925.1_ASM2429692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024296925.1_ASM2429692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:04,371] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:04,383] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:04,384] [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_001308855.1	s__Pseudomonas_E sp001308855	99.9915	2428	2442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.04	96.24	0.91	0.89	3	conclusive
GCF_018449725.1	s__Pseudomonas_E sp018449725	92.5047	2031	2442	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_003732705.1	s__Pseudomonas_E frederiksbergensis_F	91.862	2051	2442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.43	98.43	0.94	0.94	2	-
GCF_003732665.1	s__Pseudomonas_E frederiksbergensis_G	91.1054	1997	2442	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_012935755.1	s__Pseudomonas_E sp012935755	91.0603	1953	2442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008370045.1	s__Pseudomonas_E sp008370045	90.9979	1890	2442	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_004364415.1	s__Pseudomonas_E mandelii_D	90.9128	1915	2442	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_016650815.1	s__Pseudomonas_E sp016650815	90.1423	1808	2442	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_016651105.1	s__Pseudomonas_E sp016651105	89.918	1689	2442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.89	97.89	0.73	0.73	2	-
GCF_006438925.1	s__Pseudomonas_E mandelii_C	88.3795	1650	2442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	96.81	0.87	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:04,385] [INFO] GTDB search result was written to GCF_024296925.1_ASM2429692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:04,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:04,389] [INFO] DFAST_QC result json was written to GCF_024296925.1_ASM2429692v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:04,389] [INFO] DFAST_QC completed!
[2024-01-24 11:00:04,389] [INFO] Total running time: 0h2m51s