[2024-01-24 13:27:43,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:43,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:43,183] [INFO] DQC Reference Directory: /var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference
[2024-01-24 13:27:44,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:44,415] [INFO] Task started: Prodigal
[2024-01-24 13:27:44,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg93285016-2db6-48c4-acb2-a5a41a1d0d2b/GCF_000621245.1_ASM62124v1_genomic.fna.gz | prodigal -d GCF_000621245.1_ASM62124v1_genomic.fna/cds.fna -a GCF_000621245.1_ASM62124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:07,223] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:07,224] [INFO] Task started: HMMsearch
[2024-01-24 13:28:07,224] [INFO] Running command: hmmsearch --tblout GCF_000621245.1_ASM62124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference/reference_markers.hmm GCF_000621245.1_ASM62124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:07,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:07,716] [INFO] Found 6/6 markers.
[2024-01-24 13:28:07,770] [INFO] Query marker FASTA was written to GCF_000621245.1_ASM62124v1_genomic.fna/markers.fasta
[2024-01-24 13:28:07,771] [INFO] Task started: Blastn
[2024-01-24 13:28:07,771] [INFO] Running command: blastn -query GCF_000621245.1_ASM62124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference/reference_markers.fasta -out GCF_000621245.1_ASM62124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:08,785] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:08,788] [INFO] Selected 27 target genomes.
[2024-01-24 13:28:08,788] [INFO] Target genome list was writen to GCF_000621245.1_ASM62124v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:08,811] [INFO] Task started: fastANI
[2024-01-24 13:28:08,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg93285016-2db6-48c4-acb2-a5a41a1d0d2b/GCF_000621245.1_ASM62124v1_genomic.fna.gz --refList GCF_000621245.1_ASM62124v1_genomic.fna/target_genomes.txt --output GCF_000621245.1_ASM62124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:42,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:42,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:42,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:42,925] [INFO] Found 25 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:42,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:42,925] [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 monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	100.0	2057	2064	95	conclusive
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	99.9762	2009	2064	95	conclusive
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	90.6709	1523	2064	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	90.6603	1550	2064	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	90.6521	1555	2064	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	90.0272	1500	2064	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	89.0728	1429	2064	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	88.9534	1413	2064	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.7934	1385	2064	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.7615	1307	2064	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.6377	1322	2064	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	87.4867	1431	2064	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.3596	1396	2064	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	87.2271	1370	2064	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	86.6123	1407	2064	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	86.5876	1383	2064	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	86.4966	1270	2064	95	below_threshold
Pseudomonas parafulva	strain=NBRC 16636	GCA_000730645.1	157782	157782	suspected-type	True	85.8251	1213	2064	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	85.7753	1250	2064	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	81.0633	944	2064	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	81.0465	913	2064	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	81.0373	945	2064	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	80.6083	732	2064	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	79.298	605	2064	95	below_threshold
Saccharospirillum alexandrii	strain=LZ-5	GCA_004000275.1	2448477	2448477	type	True	75.6873	81	2064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:42,927] [INFO] DFAST Taxonomy check result was written to GCF_000621245.1_ASM62124v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:42,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:42,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:42,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference/checkm_data
[2024-01-24 13:28:42,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:42,988] [INFO] Task started: CheckM
[2024-01-24 13:28:42,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621245.1_ASM62124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621245.1_ASM62124v1_genomic.fna/checkm_input GCF_000621245.1_ASM62124v1_genomic.fna/checkm_result
[2024-01-24 13:29:46,499] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:46,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:46,532] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:46,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:46,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621245.1_ASM62124v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:46,533] [INFO] Task started: Blastn
[2024-01-24 13:29:46,533] [INFO] Running command: blastn -query GCF_000621245.1_ASM62124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga71995c8-535e-47c2-a3f7-afed27549f4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621245.1_ASM62124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:48,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:48,445] [INFO] Selected 23 target genomes.
[2024-01-24 13:29:48,445] [INFO] Target genome list was writen to GCF_000621245.1_ASM62124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:48,468] [INFO] Task started: fastANI
[2024-01-24 13:29:48,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg93285016-2db6-48c4-acb2-a5a41a1d0d2b/GCF_000621245.1_ASM62124v1_genomic.fna.gz --refList GCF_000621245.1_ASM62124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621245.1_ASM62124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:24,147] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:24,176] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:24,177] [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_000730605.1	s__Pseudomonas_E monteilii	99.9762	2009	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	conclusive
GCF_000708715.2	s__Pseudomonas_E putida_R	90.9343	1525	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.68	95.68	0.85	0.85	2	-
GCF_002356095.1	s__Pseudomonas_E putida_H	90.5895	1658	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.35	0.91	0.82	20	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	90.4935	1497	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_013393325.1	s__Pseudomonas_E putida_P	90.4305	1538	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	99.27	0.91	0.82	10	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	90.2403	1434	2064	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_009932335.1	s__Pseudomonas_E asiatica	90.2382	1525	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	90.1252	1455	2064	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_002165135.1	s__Pseudomonas_E sp002165135	90.0962	1436	2064	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_015680405.1	s__Pseudomonas_E pudica	90.0837	1464	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_900277125.1	s__Pseudomonas_E inefficax	90.0226	1501	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_002113165.1	s__Pseudomonas_E sp002113165	89.8143	1483	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	89.5773	1355	2064	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_003205205.1	s__Pseudomonas_E sp003205205	89.2914	1451	2064	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_013179515.1	s__Pseudomonas_E sp013179515	89.2252	1314	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_002906855.1	s__Pseudomonas_E putida_N	88.0538	1469	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	87.9767	1440	2064	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_003097235.1	s__Pseudomonas_E sp003097235	87.7968	1409	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003428805.1	s__Pseudomonas_E sp003428805	87.5476	1477	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_001320525.1	s__Pseudomonas_E sp001320525	86.9198	1419	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	98.78	0.89	0.86	10	-
GCF_000621225.1	s__Pseudomonas_E mosselii	86.7436	1374	2064	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_003231275.1	s__Pseudomonas_E huaxiensis	83.0902	1172	2064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
GCF_013523055.1	s__Pseudomonas_E capeferrum_A	82.844	1120	2064	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 13:30:24,179] [INFO] GTDB search result was written to GCF_000621245.1_ASM62124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:24,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:24,184] [INFO] DFAST_QC result json was written to GCF_000621245.1_ASM62124v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:24,184] [INFO] DFAST_QC completed!
[2024-01-24 13:30:24,184] [INFO] Total running time: 0h2m41s