[2024-01-24 12:09:05,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference
[2024-01-24 12:09:06,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,622] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg376f0091-0808-4933-9b95-e2e9888e2be5/GCF_017939625.1_ASM1793962v1_genomic.fna.gz | prodigal -d GCF_017939625.1_ASM1793962v1_genomic.fna/cds.fna -a GCF_017939625.1_ASM1793962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:17,759] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:17,760] [INFO] Task started: HMMsearch
[2024-01-24 12:09:17,760] [INFO] Running command: hmmsearch --tblout GCF_017939625.1_ASM1793962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference/reference_markers.hmm GCF_017939625.1_ASM1793962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:18,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:18,023] [INFO] Found 6/6 markers.
[2024-01-24 12:09:18,052] [INFO] Query marker FASTA was written to GCF_017939625.1_ASM1793962v1_genomic.fna/markers.fasta
[2024-01-24 12:09:18,053] [INFO] Task started: Blastn
[2024-01-24 12:09:18,053] [INFO] Running command: blastn -query GCF_017939625.1_ASM1793962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference/reference_markers.fasta -out GCF_017939625.1_ASM1793962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:19,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:19,074] [INFO] Selected 20 target genomes.
[2024-01-24 12:09:19,074] [INFO] Target genome list was writen to GCF_017939625.1_ASM1793962v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:19,082] [INFO] Task started: fastANI
[2024-01-24 12:09:19,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg376f0091-0808-4933-9b95-e2e9888e2be5/GCF_017939625.1_ASM1793962v1_genomic.fna.gz --refList GCF_017939625.1_ASM1793962v1_genomic.fna/target_genomes.txt --output GCF_017939625.1_ASM1793962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:35,734] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:35,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:35,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:35,758] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:35,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:35,759] [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
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	100.0	1194	1194	95	conclusive
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	84.7009	761	1194	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	82.4119	616	1194	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	82.2762	699	1194	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	82.2471	733	1194	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	82.2274	732	1194	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	82.2075	685	1194	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	82.1013	641	1194	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	81.784	660	1194	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.6101	641	1194	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	81.5302	592	1194	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	81.4351	728	1194	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.2931	689	1194	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	81.2548	705	1194	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.1496	544	1194	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	81.1169	634	1194	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.9477	527	1194	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.8856	646	1194	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.763	664	1194	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	80.548	557	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:35,760] [INFO] DFAST Taxonomy check result was written to GCF_017939625.1_ASM1793962v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:35,761] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:35,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:35,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference/checkm_data
[2024-01-24 12:09:35,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:35,796] [INFO] Task started: CheckM
[2024-01-24 12:09:35,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017939625.1_ASM1793962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017939625.1_ASM1793962v1_genomic.fna/checkm_input GCF_017939625.1_ASM1793962v1_genomic.fna/checkm_result
[2024-01-24 12:10:14,279] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:14,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:14,300] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:14,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:14,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017939625.1_ASM1793962v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:14,301] [INFO] Task started: Blastn
[2024-01-24 12:10:14,301] [INFO] Running command: blastn -query GCF_017939625.1_ASM1793962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f44507-864d-4a71-9c89-0b35e9acaa89/dqc_reference/reference_markers_gtdb.fasta -out GCF_017939625.1_ASM1793962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:16,310] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:16,315] [INFO] Selected 19 target genomes.
[2024-01-24 12:10:16,315] [INFO] Target genome list was writen to GCF_017939625.1_ASM1793962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:16,344] [INFO] Task started: fastANI
[2024-01-24 12:10:16,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg376f0091-0808-4933-9b95-e2e9888e2be5/GCF_017939625.1_ASM1793962v1_genomic.fna.gz --refList GCF_017939625.1_ASM1793962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017939625.1_ASM1793962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:33,251] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:33,270] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:33,270] [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_017939625.1	s__Pseudoxanthomonas_A helianthi	100.0	1194	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	84.6934	762	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427635.1	s__Pseudoxanthomonas_A sp001427635	82.4647	682	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	82.4297	653	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	82.3157	742	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093445.1	s__Pseudoxanthomonas_A japonensis	82.2705	701	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	82.2481	730	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093385.1	s__Pseudoxanthomonas_A mexicana	82.2423	682	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	82.145	700	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	82.1217	768	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCF_014851805.1	s__Pseudoxanthomonas_A sp014851805	81.9347	701	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	81.6221	633	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429615.1	s__Stenotrophomonas_A sp002429615	81.4572	553	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	81.4033	698	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_900104085.1	s__Pseudoxanthomonas_A sp900104085	81.2973	699	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	81.1402	671	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	80.9848	524	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	80.9379	612	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	80.8982	645	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:33,271] [INFO] GTDB search result was written to GCF_017939625.1_ASM1793962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:33,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:33,277] [INFO] DFAST_QC result json was written to GCF_017939625.1_ASM1793962v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:33,277] [INFO] DFAST_QC completed!
[2024-01-24 12:10:33,277] [INFO] Total running time: 0h1m28s