[2024-01-24 11:34:42,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference
[2024-01-24 11:34:43,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:43,782] [INFO] Task started: Prodigal
[2024-01-24 11:34:43,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg895f3475-a65a-4cc2-8c78-2d00b64fc015/GCF_014268585.2_ASM1426858v2_genomic.fna.gz | prodigal -d GCF_014268585.2_ASM1426858v2_genomic.fna/cds.fna -a GCF_014268585.2_ASM1426858v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:05,910] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:05,911] [INFO] Task started: HMMsearch
[2024-01-24 11:35:05,911] [INFO] Running command: hmmsearch --tblout GCF_014268585.2_ASM1426858v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference/reference_markers.hmm GCF_014268585.2_ASM1426858v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:06,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:06,260] [INFO] Found 6/6 markers.
[2024-01-24 11:35:06,307] [INFO] Query marker FASTA was written to GCF_014268585.2_ASM1426858v2_genomic.fna/markers.fasta
[2024-01-24 11:35:06,307] [INFO] Task started: Blastn
[2024-01-24 11:35:06,307] [INFO] Running command: blastn -query GCF_014268585.2_ASM1426858v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference/reference_markers.fasta -out GCF_014268585.2_ASM1426858v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:07,316] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:07,320] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:07,320] [INFO] Target genome list was writen to GCF_014268585.2_ASM1426858v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:07,325] [INFO] Task started: fastANI
[2024-01-24 11:35:07,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg895f3475-a65a-4cc2-8c78-2d00b64fc015/GCF_014268585.2_ASM1426858v2_genomic.fna.gz --refList GCF_014268585.2_ASM1426858v2_genomic.fna/target_genomes.txt --output GCF_014268585.2_ASM1426858v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,564] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:31,580] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:31,580] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:31,581] [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 iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	100.0	2024	2024	95	inconclusive
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	96.5818	1793	2024	95	inconclusive
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	96.1012	1766	2024	95	inconclusive
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	95.6196	1715	2024	95	inconclusive
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	88.7385	1667	2024	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	88.5836	1684	2024	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.5243	1654	2024	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	88.4932	1620	2024	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.3991	1636	2024	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.1841	1607	2024	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.5372	1520	2024	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	87.5169	1574	2024	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.6181	1247	2024	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.954	829	2024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,582] [INFO] DFAST Taxonomy check result was written to GCF_014268585.2_ASM1426858v2_genomic.fna/tc_result.tsv
[2024-01-24 11:35:31,583] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:31,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:31,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference/checkm_data
[2024-01-24 11:35:31,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:31,643] [INFO] Task started: CheckM
[2024-01-24 11:35:31,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268585.2_ASM1426858v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268585.2_ASM1426858v2_genomic.fna/checkm_input GCF_014268585.2_ASM1426858v2_genomic.fna/checkm_result
[2024-01-24 11:36:37,882] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:37,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:37,902] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:37,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:37,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268585.2_ASM1426858v2_genomic.fna/markers.fasta)
[2024-01-24 11:36:37,903] [INFO] Task started: Blastn
[2024-01-24 11:36:37,904] [INFO] Running command: blastn -query GCF_014268585.2_ASM1426858v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f9e69a-937f-4dc5-8252-1a8b80b4dfce/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268585.2_ASM1426858v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:39,740] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:39,743] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:39,743] [INFO] Target genome list was writen to GCF_014268585.2_ASM1426858v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:39,749] [INFO] Task started: fastANI
[2024-01-24 11:36:39,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg895f3475-a65a-4cc2-8c78-2d00b64fc015/GCF_014268585.2_ASM1426858v2_genomic.fna.gz --refList GCF_014268585.2_ASM1426858v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268585.2_ASM1426858v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:57,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:57,291] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:57,291] [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_004801935.1	s__Pseudomonas_E atacamensis	96.5818	1793	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	conclusive
GCF_001605965.1	s__Pseudomonas_E koreensis_C	95.1673	1801	2024	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_000817895.1	s__Pseudomonas_E fluorescens_AO	94.4385	1755	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	92.7007	1693	2024	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_900105805.1	s__Pseudomonas_E moraviensis_A	92.657	1768	2024	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	88.7035	1672	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.81	0.93	0.92	8	-
GCF_900582195.1	s__Pseudomonas_E sp900582195	88.5494	1636	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.42	0.95	0.95	2	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	88.0267	1587	2024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:57,293] [INFO] GTDB search result was written to GCF_014268585.2_ASM1426858v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:57,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:57,297] [INFO] DFAST_QC result json was written to GCF_014268585.2_ASM1426858v2_genomic.fna/dqc_result.json
[2024-01-24 11:36:57,297] [INFO] DFAST_QC completed!
[2024-01-24 11:36:57,297] [INFO] Total running time: 0h2m15s