[2024-01-24 14:46:56,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:56,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:56,216] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference
[2024-01-24 14:46:57,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:57,680] [INFO] Task started: Prodigal
[2024-01-24 14:46:57,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg38e45f06-c3e0-4ca6-b0bf-09daa10a4647/GCF_014269205.2_ASM1426920v2_genomic.fna.gz | prodigal -d GCF_014269205.2_ASM1426920v2_genomic.fna/cds.fna -a GCF_014269205.2_ASM1426920v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:28,134] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:28,134] [INFO] Task started: HMMsearch
[2024-01-24 14:47:28,135] [INFO] Running command: hmmsearch --tblout GCF_014269205.2_ASM1426920v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference/reference_markers.hmm GCF_014269205.2_ASM1426920v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:28,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:28,503] [INFO] Found 6/6 markers.
[2024-01-24 14:47:28,553] [INFO] Query marker FASTA was written to GCF_014269205.2_ASM1426920v2_genomic.fna/markers.fasta
[2024-01-24 14:47:28,553] [INFO] Task started: Blastn
[2024-01-24 14:47:28,553] [INFO] Running command: blastn -query GCF_014269205.2_ASM1426920v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference/reference_markers.fasta -out GCF_014269205.2_ASM1426920v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:29,627] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:29,630] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:29,631] [INFO] Target genome list was writen to GCF_014269205.2_ASM1426920v2_genomic.fna/target_genomes.txt
[2024-01-24 14:47:29,639] [INFO] Task started: fastANI
[2024-01-24 14:47:29,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e45f06-c3e0-4ca6-b0bf-09daa10a4647/GCF_014269205.2_ASM1426920v2_genomic.fna.gz --refList GCF_014269205.2_ASM1426920v2_genomic.fna/target_genomes.txt --output GCF_014269205.2_ASM1426920v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:54,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:54,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:54,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:55,008] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:55,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:55,008] [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 kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	100.0	2040	2042	95	conclusive
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	90.6087	1519	2042	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	90.5865	1701	2042	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.6388	1402	2042	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.5932	1334	2042	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	87.5548	1547	2042	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	87.4867	1552	2042	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	87.4575	1535	2042	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	87.2548	1448	2042	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	87.2263	1472	2042	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	86.902	1329	2042	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	86.8976	1348	2042	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.8136	1394	2042	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.7009	1362	2042	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	86.0648	1326	2042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:55,010] [INFO] DFAST Taxonomy check result was written to GCF_014269205.2_ASM1426920v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:55,011] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:55,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:55,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference/checkm_data
[2024-01-24 14:47:55,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:55,074] [INFO] Task started: CheckM
[2024-01-24 14:47:55,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014269205.2_ASM1426920v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014269205.2_ASM1426920v2_genomic.fna/checkm_input GCF_014269205.2_ASM1426920v2_genomic.fna/checkm_result
[2024-01-24 14:49:18,005] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:18,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:18,027] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:18,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:18,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014269205.2_ASM1426920v2_genomic.fna/markers.fasta)
[2024-01-24 14:49:18,028] [INFO] Task started: Blastn
[2024-01-24 14:49:18,028] [INFO] Running command: blastn -query GCF_014269205.2_ASM1426920v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4868a09-c42e-4842-b546-3cbd9bb8b44d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014269205.2_ASM1426920v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:19,737] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:19,741] [INFO] Selected 24 target genomes.
[2024-01-24 14:49:19,741] [INFO] Target genome list was writen to GCF_014269205.2_ASM1426920v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:19,771] [INFO] Task started: fastANI
[2024-01-24 14:49:19,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e45f06-c3e0-4ca6-b0bf-09daa10a4647/GCF_014269205.2_ASM1426920v2_genomic.fna.gz --refList GCF_014269205.2_ASM1426920v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014269205.2_ASM1426920v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:59,611] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:59,633] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:59,634] [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_002736125.1	s__Pseudomonas_E putida_M	97.5571	1829	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	conclusive
GCF_000731675.1	s__Pseudomonas_E capeferrum	90.5844	1703	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	88.1092	1476	2042	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_009932335.1	s__Pseudomonas_E asiatica	87.815	1488	2042	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_000708715.2	s__Pseudomonas_E putida_R	87.6492	1560	2042	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_013373935.1	s__Pseudomonas_E sp002438125	87.5928	1334	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_000498395.2	s__Pseudomonas_E putida_Q	87.4954	1595	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	97.78	0.93	0.90	5	-
GCF_000412675.1	s__Pseudomonas_E putida	87.4737	1569	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	87.373	1480	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	87.3245	1416	2042	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_002112505.1	s__Pseudomonas_E sp002112505	87.3133	1464	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_003097235.1	s__Pseudomonas_E sp003097235	87.2964	1429	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003627215.1	s__Pseudomonas_E sp001422615	87.2259	1446	2042	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_000282535.1	s__Pseudomonas_E sp000282535	87.1519	1280	2042	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	87.0527	1339	2042	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	86.9983	1443	2042	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_003671955.1	s__Pseudomonas_E hunanensis	86.7705	1498	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_000019445.1	s__Pseudomonas_E putida_E	86.5122	1357	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_009932375.1	s__Pseudomonas_E juntendi	86.1373	1240	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	86.0828	1325	2042	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_015680235.1	s__Pseudomonas_E guariconensis_A	85.6585	1233	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.73	0.91	0.90	4	-
GCF_007677725.1	s__Pseudomonas_E sp003445295	84.8309	1239	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	98.48	0.95	0.95	2	-
GCF_009908285.1	s__Pseudomonas_E sp009908285	80.9751	990	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.16	99.16	0.95	0.95	2	-
GCF_000474255.1	s__Pseudomonas_F alcaligenes_A	80.8447	896	2042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:59,636] [INFO] GTDB search result was written to GCF_014269205.2_ASM1426920v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:59,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:59,642] [INFO] DFAST_QC result json was written to GCF_014269205.2_ASM1426920v2_genomic.fna/dqc_result.json
[2024-01-24 14:49:59,642] [INFO] DFAST_QC completed!
[2024-01-24 14:49:59,642] [INFO] Total running time: 0h3m3s