[2024-01-24 14:22:04,512] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference
[2024-01-24 14:22:05,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,877] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg20f5812c-8b0d-4227-ad79-ce5311986921/GCF_014268655.2_ASM1426865v2_genomic.fna.gz | prodigal -d GCF_014268655.2_ASM1426865v2_genomic.fna/cds.fna -a GCF_014268655.2_ASM1426865v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:30,849] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:30,850] [INFO] Task started: HMMsearch
[2024-01-24 14:22:30,850] [INFO] Running command: hmmsearch --tblout GCF_014268655.2_ASM1426865v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference/reference_markers.hmm GCF_014268655.2_ASM1426865v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:31,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:31,220] [INFO] Found 6/6 markers.
[2024-01-24 14:22:31,268] [INFO] Query marker FASTA was written to GCF_014268655.2_ASM1426865v2_genomic.fna/markers.fasta
[2024-01-24 14:22:31,268] [INFO] Task started: Blastn
[2024-01-24 14:22:31,268] [INFO] Running command: blastn -query GCF_014268655.2_ASM1426865v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference/reference_markers.fasta -out GCF_014268655.2_ASM1426865v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:32,331] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:32,334] [INFO] Selected 18 target genomes.
[2024-01-24 14:22:32,335] [INFO] Target genome list was writen to GCF_014268655.2_ASM1426865v2_genomic.fna/target_genomes.txt
[2024-01-24 14:22:32,346] [INFO] Task started: fastANI
[2024-01-24 14:22:32,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg20f5812c-8b0d-4227-ad79-ce5311986921/GCF_014268655.2_ASM1426865v2_genomic.fna.gz --refList GCF_014268655.2_ASM1426865v2_genomic.fna/target_genomes.txt --output GCF_014268655.2_ASM1426865v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:00,173] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:00,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:00,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:00,191] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:00,191] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:00,192] [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 marvdashtae	strain=SWRI102	GCA_014268655.2	2745500	2745500	type	True	100.0	1958	1959	95	conclusive
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	88.4876	1625	1959	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	88.3496	1564	1959	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	88.3278	1547	1959	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	88.2354	1589	1959	95	below_threshold
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	88.1898	1596	1959	95	below_threshold
Pseudomonas bijieensis	strain=L22-9	GCA_013347965.1	2681983	2681983	type	True	87.9891	1599	1959	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	87.7892	1534	1959	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	87.0672	1541	1959	95	below_threshold
Pseudomonas tehranensis	strain=SWRI196	GCA_014268615.1	2745502	2745502	type	True	86.8757	1309	1959	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	84.1481	1187	1959	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	84.0238	1207	1959	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	83.6518	1227	1959	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	83.5599	1187	1959	95	below_threshold
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	83.4617	1175	1959	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	83.4075	1214	1959	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	83.1834	1194	1959	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.108	1109	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:00,197] [INFO] DFAST Taxonomy check result was written to GCF_014268655.2_ASM1426865v2_genomic.fna/tc_result.tsv
[2024-01-24 14:23:00,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:00,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:00,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference/checkm_data
[2024-01-24 14:23:00,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:00,261] [INFO] Task started: CheckM
[2024-01-24 14:23:00,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268655.2_ASM1426865v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268655.2_ASM1426865v2_genomic.fna/checkm_input GCF_014268655.2_ASM1426865v2_genomic.fna/checkm_result
[2024-01-24 14:24:09,696] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:09,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:09,723] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:09,723] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:09,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268655.2_ASM1426865v2_genomic.fna/markers.fasta)
[2024-01-24 14:24:09,724] [INFO] Task started: Blastn
[2024-01-24 14:24:09,724] [INFO] Running command: blastn -query GCF_014268655.2_ASM1426865v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8227f392-ee73-40b9-9d31-b1cd1bb7373d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268655.2_ASM1426865v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:11,674] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:11,678] [INFO] Selected 18 target genomes.
[2024-01-24 14:24:11,678] [INFO] Target genome list was writen to GCF_014268655.2_ASM1426865v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:11,699] [INFO] Task started: fastANI
[2024-01-24 14:24:11,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg20f5812c-8b0d-4227-ad79-ce5311986921/GCF_014268655.2_ASM1426865v2_genomic.fna.gz --refList GCF_014268655.2_ASM1426865v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268655.2_ASM1426865v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:40,932] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:40,946] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:40,947] [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_014268655.2	s__Pseudomonas_E sp014268655	100.0	1958	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	96.17	0.92	0.88	3	conclusive
GCF_019141525.1	s__Pseudomonas_E fluorescens_T	88.6618	1640	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.80	98.76	0.93	0.91	4	-
GCF_013608025.1	s__Pseudomonas_E neoaurantiaca	88.6334	1600	1959	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_001269655.1	s__Pseudomonas_E thivervalensis	88.4836	1626	1959	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_900581005.1	s__Pseudomonas_E sp900581005	88.4019	1585	1959	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_001269885.1	s__Pseudomonas_E kilonensis	88.3441	1545	1959	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_014268745.2	s__Pseudomonas_E sp014268745	88.3354	1566	1959	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_001307275.1	s__Pseudomonas_E fluorescens_AA	88.3106	1580	1959	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_008801605.1	s__Pseudomonas_E brassicacearum	88.2043	1595	1959	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_009601685.2	s__Pseudomonas_E kilonensis_B	88.0878	1572	1959	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_018325905.1	s__Pseudomonas_E sp018325905	87.9637	1568	1959	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	87.909	1566	1959	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_004786035.1	s__Pseudomonas_E viciae	87.7816	1535	1959	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_000585995.1	s__Pseudomonas_E brassicacearum_A	87.6947	1586	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.55	95.52	0.86	0.84	3	-
GCF_000281895.1	s__Pseudomonas_E fluorescens_S	87.2429	1553	1959	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_001605965.1	s__Pseudomonas_E koreensis_C	83.6383	1221	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	-
GCF_900105805.1	s__Pseudomonas_E moraviensis_A	83.5567	1221	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_900105485.1	s__Pseudomonas_E granadensis	83.3803	1215	1959	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:40,948] [INFO] GTDB search result was written to GCF_014268655.2_ASM1426865v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:40,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:40,953] [INFO] DFAST_QC result json was written to GCF_014268655.2_ASM1426865v2_genomic.fna/dqc_result.json
[2024-01-24 14:24:40,953] [INFO] DFAST_QC completed!
[2024-01-24 14:24:40,953] [INFO] Total running time: 0h2m36s