[2024-01-24 14:46:35,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,085] [INFO] DQC Reference Directory: /var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference
[2024-01-24 14:46:36,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,330] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg0546bbe9-f269-4308-b13c-645c4482bee7/GCF_019139895.1_ASM1913989v1_genomic.fna.gz | prodigal -d GCF_019139895.1_ASM1913989v1_genomic.fna/cds.fna -a GCF_019139895.1_ASM1913989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:05,183] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:05,183] [INFO] Task started: HMMsearch
[2024-01-24 14:47:05,184] [INFO] Running command: hmmsearch --tblout GCF_019139895.1_ASM1913989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference/reference_markers.hmm GCF_019139895.1_ASM1913989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:05,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:05,541] [INFO] Found 6/6 markers.
[2024-01-24 14:47:05,607] [INFO] Query marker FASTA was written to GCF_019139895.1_ASM1913989v1_genomic.fna/markers.fasta
[2024-01-24 14:47:05,608] [INFO] Task started: Blastn
[2024-01-24 14:47:05,608] [INFO] Running command: blastn -query GCF_019139895.1_ASM1913989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference/reference_markers.fasta -out GCF_019139895.1_ASM1913989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:06,736] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:06,741] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:06,742] [INFO] Target genome list was writen to GCF_019139895.1_ASM1913989v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:06,751] [INFO] Task started: fastANI
[2024-01-24 14:47:06,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg0546bbe9-f269-4308-b13c-645c4482bee7/GCF_019139895.1_ASM1913989v1_genomic.fna.gz --refList GCF_019139895.1_ASM1913989v1_genomic.fna/target_genomes.txt --output GCF_019139895.1_ASM1913989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:33,490] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:33,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:33,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:33,512] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:33,512] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:47:33,512] [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 fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	100.0	2047	2049	95	inconclusive
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	95.4978	1722	2049	95	inconclusive
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	88.7497	1429	2049	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	88.6055	1449	2049	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	88.3293	1442	2049	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	88.2168	1423	2049	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	88.0417	1444	2049	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	88.0209	1442	2049	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.8647	1280	2049	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.8446	1354	2049	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	87.7261	1415	2049	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	86.5169	1383	2049	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.4268	1246	2049	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	85.7281	1291	2049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:33,514] [INFO] DFAST Taxonomy check result was written to GCF_019139895.1_ASM1913989v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:33,515] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:33,515] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:33,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference/checkm_data
[2024-01-24 14:47:33,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:33,585] [INFO] Task started: CheckM
[2024-01-24 14:47:33,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019139895.1_ASM1913989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019139895.1_ASM1913989v1_genomic.fna/checkm_input GCF_019139895.1_ASM1913989v1_genomic.fna/checkm_result
[2024-01-24 14:49:00,267] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:00,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:00,288] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:00,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:00,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019139895.1_ASM1913989v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:00,290] [INFO] Task started: Blastn
[2024-01-24 14:49:00,290] [INFO] Running command: blastn -query GCF_019139895.1_ASM1913989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd11d1f34-9544-41f2-bfb4-be9725aab138/dqc_reference/reference_markers_gtdb.fasta -out GCF_019139895.1_ASM1913989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:02,388] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:02,393] [INFO] Selected 14 target genomes.
[2024-01-24 14:49:02,393] [INFO] Target genome list was writen to GCF_019139895.1_ASM1913989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:02,406] [INFO] Task started: fastANI
[2024-01-24 14:49:02,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg0546bbe9-f269-4308-b13c-645c4482bee7/GCF_019139895.1_ASM1913989v1_genomic.fna.gz --refList GCF_019139895.1_ASM1913989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019139895.1_ASM1913989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:29,359] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:29,371] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:29,372] [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_019139835.1	s__Pseudomonas_E sp019139835	95.4925	1722	2049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.50	95.50	0.87	0.87	2	conclusive
GCF_003231305.1	s__Pseudomonas_E sichuanensis	88.7172	1433	2049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	88.5957	1449	2049	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_015354575.1	s__Pseudomonas_E sp015354575	88.5175	1494	2049	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_016861355.1	s__Pseudomonas_E sp001259595	88.4222	1474	2049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_003205295.1	s__Pseudomonas_E mosselii_B	88.4111	1431	2049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_000621225.1	s__Pseudomonas_E mosselii	88.2309	1422	2049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	88.1316	1368	2049	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_019139675.1	s__Pseudomonas_E sp019139675	88.0573	1444	2049	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_014268885.2	s__Pseudomonas_E sp014268885	87.9988	1443	2049	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_011752525.1	s__Pseudomonas_E sp011752525	87.871	1349	2049	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_900110655.1	s__Pseudomonas_E soli	87.7615	1411	2049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	87.2235	1371	2049	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_001320245.1	s__Pseudomonas_E sp001320245	86.6589	1371	2049	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 14:49:29,373] [INFO] GTDB search result was written to GCF_019139895.1_ASM1913989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:29,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:29,377] [INFO] DFAST_QC result json was written to GCF_019139895.1_ASM1913989v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:29,378] [INFO] DFAST_QC completed!
[2024-01-24 14:49:29,378] [INFO] Total running time: 0h2m54s