[2024-01-24 13:40:39,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:39,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:39,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference
[2024-01-24 13:40:40,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:40,941] [INFO] Task started: Prodigal
[2024-01-24 13:40:40,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg581b2a2a-2e10-4719-a716-2cc3090054c9/GCF_024169545.1_ASM2416954v1_genomic.fna.gz | prodigal -d GCF_024169545.1_ASM2416954v1_genomic.fna/cds.fna -a GCF_024169545.1_ASM2416954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,052] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,053] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,053] [INFO] Running command: hmmsearch --tblout GCF_024169545.1_ASM2416954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference/reference_markers.hmm GCF_024169545.1_ASM2416954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:05,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:05,436] [INFO] Found 6/6 markers.
[2024-01-24 13:41:05,489] [INFO] Query marker FASTA was written to GCF_024169545.1_ASM2416954v1_genomic.fna/markers.fasta
[2024-01-24 13:41:05,490] [INFO] Task started: Blastn
[2024-01-24 13:41:05,490] [INFO] Running command: blastn -query GCF_024169545.1_ASM2416954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference/reference_markers.fasta -out GCF_024169545.1_ASM2416954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,383] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,386] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:06,386] [INFO] Target genome list was writen to GCF_024169545.1_ASM2416954v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:06,394] [INFO] Task started: fastANI
[2024-01-24 13:41:06,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg581b2a2a-2e10-4719-a716-2cc3090054c9/GCF_024169545.1_ASM2416954v1_genomic.fna.gz --refList GCF_024169545.1_ASM2416954v1_genomic.fna/target_genomes.txt --output GCF_024169545.1_ASM2416954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:36,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:36,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:36,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:36,286] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:36,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:36,286] [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=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	88.8024	1690	2159	95	below_threshold
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	88.7159	1673	2159	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	88.6689	1668	2159	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	88.2001	1584	2159	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	88.196	1580	2159	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	88.1513	1561	2159	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.2647	1559	2159	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.1556	1469	2159	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.1518	1475	2159	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.5268	1495	2159	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.407	1444	2159	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	86.1021	1450	2159	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	85.9735	1505	2159	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.9618	1497	2159	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	85.8937	1477	2159	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	85.8871	1486	2159	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.1061	1289	2159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,287] [INFO] DFAST Taxonomy check result was written to GCF_024169545.1_ASM2416954v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:36,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:36,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:36,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference/checkm_data
[2024-01-24 13:41:36,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:36,346] [INFO] Task started: CheckM
[2024-01-24 13:41:36,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024169545.1_ASM2416954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024169545.1_ASM2416954v1_genomic.fna/checkm_input GCF_024169545.1_ASM2416954v1_genomic.fna/checkm_result
[2024-01-24 13:42:48,776] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:48,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:48,793] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:48,794] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:48,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024169545.1_ASM2416954v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:48,794] [INFO] Task started: Blastn
[2024-01-24 13:42:48,794] [INFO] Running command: blastn -query GCF_024169545.1_ASM2416954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5115b661-c18a-454a-b35d-8712f255e8e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024169545.1_ASM2416954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:50,405] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:50,408] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:50,408] [INFO] Target genome list was writen to GCF_024169545.1_ASM2416954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:50,442] [INFO] Task started: fastANI
[2024-01-24 13:42:50,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg581b2a2a-2e10-4719-a716-2cc3090054c9/GCF_024169545.1_ASM2416954v1_genomic.fna.gz --refList GCF_024169545.1_ASM2416954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024169545.1_ASM2416954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:15,566] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:15,574] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:15,574] [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_000282415.1	s__Pseudomonas_E sp000282415	97.1493	1858	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.21	0.89	0.87	6	conclusive
GCF_902498065.1	s__Pseudomonas_E fluorescens_BJ	92.7672	1748	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.24	0.94	0.93	3	-
GCF_002091715.1	s__Pseudomonas_E migulae	91.3463	1762	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.09	0.95	0.90	3	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	91.3197	1750	2159	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_000293885.2	s__Pseudomonas_E fluorescens_B	90.9851	1784	2159	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_902497785.1	s__Pseudomonas_E fluorescens_BO	89.4451	1621	2159	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_004136015.1	s__Pseudomonas_E sp004136015	89.1277	1655	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.14	95.84	0.91	0.90	3	-
GCF_000968015.1	s__Pseudomonas_E fluorescens_W	89.1169	1676	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_003151075.1	s__Pseudomonas_E sp003151075	89.0496	1669	2159	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_900103875.1	s__Pseudomonas_E arsenicoxydans	88.4042	1608	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.47	96.47	0.86	0.86	2	-
GCF_000282495.1	s__Pseudomonas_E sp000282495	88.0911	1551	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.96	0.87	0.86	6	-
GCF_000282215.1	s__Pseudomonas_E sp000282215	87.6089	1452	2159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.42	97.42	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:15,576] [INFO] GTDB search result was written to GCF_024169545.1_ASM2416954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:15,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:15,580] [INFO] DFAST_QC result json was written to GCF_024169545.1_ASM2416954v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:15,580] [INFO] DFAST_QC completed!
[2024-01-24 13:43:15,580] [INFO] Total running time: 0h2m36s