[2024-01-24 13:46:01,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference
[2024-01-24 13:46:02,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,879] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg727c81e5-285a-4d19-8960-bba4728ff5ac/GCF_031954405.1_ASM3195440v1_genomic.fna.gz | prodigal -d GCF_031954405.1_ASM3195440v1_genomic.fna/cds.fna -a GCF_031954405.1_ASM3195440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:30,044] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:30,045] [INFO] Task started: HMMsearch
[2024-01-24 13:46:30,045] [INFO] Running command: hmmsearch --tblout GCF_031954405.1_ASM3195440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference/reference_markers.hmm GCF_031954405.1_ASM3195440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:30,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:30,434] [INFO] Found 6/6 markers.
[2024-01-24 13:46:30,492] [INFO] Query marker FASTA was written to GCF_031954405.1_ASM3195440v1_genomic.fna/markers.fasta
[2024-01-24 13:46:30,492] [INFO] Task started: Blastn
[2024-01-24 13:46:30,493] [INFO] Running command: blastn -query GCF_031954405.1_ASM3195440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference/reference_markers.fasta -out GCF_031954405.1_ASM3195440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:31,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:31,480] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:31,480] [INFO] Target genome list was writen to GCF_031954405.1_ASM3195440v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:31,491] [INFO] Task started: fastANI
[2024-01-24 13:46:31,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg727c81e5-285a-4d19-8960-bba4728ff5ac/GCF_031954405.1_ASM3195440v1_genomic.fna.gz --refList GCF_031954405.1_ASM3195440v1_genomic.fna/target_genomes.txt --output GCF_031954405.1_ASM3195440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:58,077] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:58,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:58,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:58,092] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:58,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:58,092] [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 protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	99.1025	2203	2311	95	conclusive
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	99.0944	2203	2311	95	conclusive
Pseudomonas sessilinigenes	strain=CMR12a	GCA_003850565.1	658629	658629	type	True	87.8695	1802	2311	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_019139855.1	658629	658629	type	True	87.7611	1819	2311	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	86.7802	1643	2311	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	86.7468	1667	2311	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	86.7274	1642	2311	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=LMG 5004	GCA_001269625.1	333	587753	type	True	86.6167	1644	2311	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	86.6015	1680	2311	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_007858335.1	333	587753	type	True	86.5825	1641	2311	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=ATCC 9446	GCA_002095925.1	333	587753	type	True	86.5695	1638	2311	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	83.6941	1297	2311	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.5726	1087	2311	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.5587	1153	2311	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	82.4695	1169	2311	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	81.8223	1038	2311	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.76	846	2311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:58,094] [INFO] DFAST Taxonomy check result was written to GCF_031954405.1_ASM3195440v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:58,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:58,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:58,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference/checkm_data
[2024-01-24 13:46:58,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:58,164] [INFO] Task started: CheckM
[2024-01-24 13:46:58,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031954405.1_ASM3195440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031954405.1_ASM3195440v1_genomic.fna/checkm_input GCF_031954405.1_ASM3195440v1_genomic.fna/checkm_result
[2024-01-24 13:48:12,410] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:12,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:12,434] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:12,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:12,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031954405.1_ASM3195440v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:12,435] [INFO] Task started: Blastn
[2024-01-24 13:48:12,436] [INFO] Running command: blastn -query GCF_031954405.1_ASM3195440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d70d6bc-926f-4af8-b91c-bf0dbda157c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_031954405.1_ASM3195440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:14,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:14,218] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:14,219] [INFO] Target genome list was writen to GCF_031954405.1_ASM3195440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:14,240] [INFO] Task started: fastANI
[2024-01-24 13:48:14,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg727c81e5-285a-4d19-8960-bba4728ff5ac/GCF_031954405.1_ASM3195440v1_genomic.fna.gz --refList GCF_031954405.1_ASM3195440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031954405.1_ASM3195440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:34,553] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:34,566] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:34,566] [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_000397205.1	s__Pseudomonas_E protegens	99.0944	2203	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	conclusive
GCF_003732485.1	s__Pseudomonas_E protegens_B	91.5963	2004	2311	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_013407925.2	s__Pseudomonas_E fluorescens_AP	90.9807	1912	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	98.42	0.98	0.91	6	-
GCF_001547895.1	s__Pseudomonas_E sp001547895	90.6903	1987	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
GCF_003363755.1	s__Pseudomonas_E protegens_A	90.635	1947	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.07	97.56	0.94	0.93	12	-
GCF_900105185.1	s__Pseudomonas_E saponiphila	90.4631	1851	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
GCF_000633395.1	s__Pseudomonas_E sp000633395	90.4319	2030	2311	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_009861525.1	s__Pseudomonas_E sp009861525	88.8723	1834	2311	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_009380155.1	s__Pseudomonas_E piscis	88.1944	1813	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	95.64	0.89	0.85	10	-
GCF_003850565.1	s__Pseudomonas_E sp001705835	87.862	1803	2311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.20	98.99	0.91	0.87	6	-
GCF_900107395.1	s__Pseudomonas_E sp900107395	86.3447	1570	2311	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 13:48:34,568] [INFO] GTDB search result was written to GCF_031954405.1_ASM3195440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:34,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:34,573] [INFO] DFAST_QC result json was written to GCF_031954405.1_ASM3195440v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:34,574] [INFO] DFAST_QC completed!
[2024-01-24 13:48:34,574] [INFO] Total running time: 0h2m33s