[2024-01-24 12:00:36,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference
[2024-01-24 12:00:39,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,379] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,379] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c23c704-bb5a-4020-b112-3945d9715819/GCF_025336485.1_ASM2533648v1_genomic.fna.gz | prodigal -d GCF_025336485.1_ASM2533648v1_genomic.fna/cds.fna -a GCF_025336485.1_ASM2533648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:01:13,387] [INFO] Task succeeded: Prodigal
[2024-01-24 12:01:13,387] [INFO] Task started: HMMsearch
[2024-01-24 12:01:13,387] [INFO] Running command: hmmsearch --tblout GCF_025336485.1_ASM2533648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference/reference_markers.hmm GCF_025336485.1_ASM2533648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:01:13,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:01:13,718] [INFO] Found 6/6 markers.
[2024-01-24 12:01:13,767] [INFO] Query marker FASTA was written to GCF_025336485.1_ASM2533648v1_genomic.fna/markers.fasta
[2024-01-24 12:01:13,767] [INFO] Task started: Blastn
[2024-01-24 12:01:13,768] [INFO] Running command: blastn -query GCF_025336485.1_ASM2533648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference/reference_markers.fasta -out GCF_025336485.1_ASM2533648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:14,759] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:14,763] [INFO] Selected 16 target genomes.
[2024-01-24 12:01:14,763] [INFO] Target genome list was writen to GCF_025336485.1_ASM2533648v1_genomic.fna/target_genomes.txt
[2024-01-24 12:01:14,770] [INFO] Task started: fastANI
[2024-01-24 12:01:14,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c23c704-bb5a-4020-b112-3945d9715819/GCF_025336485.1_ASM2533648v1_genomic.fna.gz --refList GCF_025336485.1_ASM2533648v1_genomic.fna/target_genomes.txt --output GCF_025336485.1_ASM2533648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:38,059] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:38,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:38,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:38,077] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:01:38,078] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:01:38,078] [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 brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	88.473	1531	2050	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	88.4481	1552	2050	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	88.4401	1539	2050	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	88.1463	1549	2050	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	87.924	1556	2050	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	87.9044	1533	2050	95	below_threshold
Pseudomonas mediterranea	strain=CFBP 5447	GCA_000774145.1	183795	183795	type	True	87.6017	1543	2050	95	below_threshold
Pseudomonas mediterranea	strain=DSM 16733	GCA_900106005.1	183795	183795	type	True	87.5873	1555	2050	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	87.173	1463	2050	95	below_threshold
Pseudomonas corrugata	strain=DSM 7228	GCA_001269905.1	47879	47879	type	True	86.9576	1548	2050	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_001411965.1	47879	47879	type	True	86.9385	1536	2050	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_003699065.1	47879	47879	type	True	86.9213	1514	2050	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	84.2502	1211	2050	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	84.0991	1208	2050	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.1206	1090	2050	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.187	808	2050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:38,079] [INFO] DFAST Taxonomy check result was written to GCF_025336485.1_ASM2533648v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:38,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:38,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:38,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference/checkm_data
[2024-01-24 12:01:38,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:38,146] [INFO] Task started: CheckM
[2024-01-24 12:01:38,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025336485.1_ASM2533648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025336485.1_ASM2533648v1_genomic.fna/checkm_input GCF_025336485.1_ASM2533648v1_genomic.fna/checkm_result
[2024-01-24 12:03:09,379] [INFO] Task succeeded: CheckM
[2024-01-24 12:03:09,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:03:09,415] [INFO] ===== Completeness check finished =====
[2024-01-24 12:03:09,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:03:09,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025336485.1_ASM2533648v1_genomic.fna/markers.fasta)
[2024-01-24 12:03:09,416] [INFO] Task started: Blastn
[2024-01-24 12:03:09,417] [INFO] Running command: blastn -query GCF_025336485.1_ASM2533648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ccce5e-c3cb-47dc-9548-35b14e198ce2/dqc_reference/reference_markers_gtdb.fasta -out GCF_025336485.1_ASM2533648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:03:11,275] [INFO] Task succeeded: Blastn
[2024-01-24 12:03:11,281] [INFO] Selected 18 target genomes.
[2024-01-24 12:03:11,281] [INFO] Target genome list was writen to GCF_025336485.1_ASM2533648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:03:11,296] [INFO] Task started: fastANI
[2024-01-24 12:03:11,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c23c704-bb5a-4020-b112-3945d9715819/GCF_025336485.1_ASM2533648v1_genomic.fna.gz --refList GCF_025336485.1_ASM2533648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025336485.1_ASM2533648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:03:39,708] [INFO] Task succeeded: fastANI
[2024-01-24 12:03:39,729] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:03:39,730] [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_008801605.1	s__Pseudomonas_E brassicacearum	88.4666	1532	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	96.48	0.95	0.86	21	-
GCF_001269885.1	s__Pseudomonas_E kilonensis	88.4293	1540	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.12	95.91	0.90	0.87	15	-
GCF_001307275.1	s__Pseudomonas_E fluorescens_AA	88.3275	1617	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.99	95.90	0.90	0.85	18	-
GCF_009601685.2	s__Pseudomonas_E kilonensis_B	88.3261	1563	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.30	99.26	0.94	0.93	4	-
GCF_900581005.1	s__Pseudomonas_E sp900581005	88.2793	1524	2050	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_018325905.1	s__Pseudomonas_E sp018325905	88.2781	1562	2050	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_001623525.1	s__Pseudomonas_E fluorescens_Q	88.1821	1533	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.03	97.11	0.90	0.89	14	-
GCF_001269655.1	s__Pseudomonas_E thivervalensis	88.1678	1546	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
GCF_014268745.2	s__Pseudomonas_E sp014268745	87.9067	1533	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.32	95.56	0.90	0.87	3	-
GCF_001023535.1	s__Pseudomonas_E chlororaphis_E	87.8898	1514	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	97.84	0.94	0.94	5	-
GCF_017968885.1	s__Pseudomonas_E sp017968885	87.824	1579	2050	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_000774145.1	s__Pseudomonas_E mediterranea	87.5905	1545	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.46	99.30	0.95	0.94	8	-
GCF_014596565.1	s__Pseudomonas_E sp000801235	87.5676	1500	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000281895.1	s__Pseudomonas_E fluorescens_S	87.4169	1507	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.50	99.50	0.99	0.99	2	-
GCF_006227205.1	s__Pseudomonas_E sp006227205	87.3533	1560	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.77	0.93	0.93	3	-
GCF_007828215.1	s__Pseudomonas_E sp007828215	87.1662	1532	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	99.65	0.96	0.95	6	-
GCF_001269905.1	s__Pseudomonas_E corrugata	86.9589	1548	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.47	0.98	0.95	7	-
GCF_001269775.1	s__Pseudomonas_E sp001269775	86.78	1458	2050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:03:39,732] [INFO] GTDB search result was written to GCF_025336485.1_ASM2533648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:03:39,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:03:39,739] [INFO] DFAST_QC result json was written to GCF_025336485.1_ASM2533648v1_genomic.fna/dqc_result.json
[2024-01-24 12:03:39,739] [INFO] DFAST_QC completed!
[2024-01-24 12:03:39,740] [INFO] Total running time: 0h3m3s