[2024-01-24 15:02:46,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:46,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:46,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference
[2024-01-24 15:02:47,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:47,915] [INFO] Task started: Prodigal
[2024-01-24 15:02:47,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg8686c1de-3b93-4766-93b4-27f809f2bac4/GCF_010093445.1_ASM1009344v1_genomic.fna.gz | prodigal -d GCF_010093445.1_ASM1009344v1_genomic.fna/cds.fna -a GCF_010093445.1_ASM1009344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:01,676] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:01,677] [INFO] Task started: HMMsearch
[2024-01-24 15:03:01,677] [INFO] Running command: hmmsearch --tblout GCF_010093445.1_ASM1009344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference/reference_markers.hmm GCF_010093445.1_ASM1009344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:02,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:02,001] [INFO] Found 6/6 markers.
[2024-01-24 15:03:02,043] [INFO] Query marker FASTA was written to GCF_010093445.1_ASM1009344v1_genomic.fna/markers.fasta
[2024-01-24 15:03:02,044] [INFO] Task started: Blastn
[2024-01-24 15:03:02,044] [INFO] Running command: blastn -query GCF_010093445.1_ASM1009344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference/reference_markers.fasta -out GCF_010093445.1_ASM1009344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:03,101] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:03,103] [INFO] Selected 19 target genomes.
[2024-01-24 15:03:03,104] [INFO] Target genome list was writen to GCF_010093445.1_ASM1009344v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:03,110] [INFO] Task started: fastANI
[2024-01-24 15:03:03,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg8686c1de-3b93-4766-93b4-27f809f2bac4/GCF_010093445.1_ASM1009344v1_genomic.fna.gz --refList GCF_010093445.1_ASM1009344v1_genomic.fna/target_genomes.txt --output GCF_010093445.1_ASM1009344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:20,565] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:20,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:20,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:20,579] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:20,579] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:20,580] [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 japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	100.0	1318	1324	95	conclusive
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	87.5797	981	1324	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	83.1128	817	1324	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	82.6031	824	1324	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.4828	854	1324	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	82.1151	703	1324	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	82.0778	760	1324	95	below_threshold
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	82.0548	773	1324	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	81.7116	636	1324	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.9442	661	1324	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.8429	688	1324	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	80.8251	670	1324	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.695	485	1324	95	below_threshold
Stenotrophomonas lactitubi	strain=M15	GCA_002803515.1	2045214	2045214	type	True	80.6143	657	1324	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	80.5619	713	1324	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	80.4208	616	1324	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	80.2918	587	1324	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	79.9652	511	1324	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	79.811	549	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:20,581] [INFO] DFAST Taxonomy check result was written to GCF_010093445.1_ASM1009344v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:20,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:20,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:20,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference/checkm_data
[2024-01-24 15:03:20,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:20,623] [INFO] Task started: CheckM
[2024-01-24 15:03:20,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093445.1_ASM1009344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093445.1_ASM1009344v1_genomic.fna/checkm_input GCF_010093445.1_ASM1009344v1_genomic.fna/checkm_result
[2024-01-24 15:04:09,769] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:09,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:09,787] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:09,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:09,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093445.1_ASM1009344v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:09,788] [INFO] Task started: Blastn
[2024-01-24 15:04:09,788] [INFO] Running command: blastn -query GCF_010093445.1_ASM1009344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg128237f7-8a56-4ebf-8856-7f46850ce5b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093445.1_ASM1009344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:11,977] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:11,980] [INFO] Selected 10 target genomes.
[2024-01-24 15:04:11,980] [INFO] Target genome list was writen to GCF_010093445.1_ASM1009344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:11,990] [INFO] Task started: fastANI
[2024-01-24 15:04:11,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg8686c1de-3b93-4766-93b4-27f809f2bac4/GCF_010093445.1_ASM1009344v1_genomic.fna.gz --refList GCF_010093445.1_ASM1009344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093445.1_ASM1009344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:22,536] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:22,545] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:22,546] [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_010093445.1	s__Pseudoxanthomonas_A japonensis	100.0	1318	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	conclusive
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	90.0235	1109	1324	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_001556105.1	s__Pseudoxanthomonas_A mexicana_A	89.4309	1010	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.72	98.63	0.92	0.88	3	-
GCF_014851805.1	s__Pseudoxanthomonas_A sp014851805	88.7971	1084	1324	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	88.7587	1075	1324	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_002863005.1	s__Pseudoxanthomonas_A sp002863005	87.6192	1016	1324	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	87.5929	978	1324	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_001427585.1	s__Pseudoxanthomonas_A sp001427585	87.2516	1038	1324	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_014852005.1	s__Pseudoxanthomonas_A sp014852005	86.9817	1024	1324	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_002862435.1	s__Macondimonas sp002862435	80.3901	115	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA5335;f__UBA5335;g__Macondimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:22,548] [INFO] GTDB search result was written to GCF_010093445.1_ASM1009344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:22,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:22,552] [INFO] DFAST_QC result json was written to GCF_010093445.1_ASM1009344v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:22,552] [INFO] DFAST_QC completed!
[2024-01-24 15:04:22,552] [INFO] Total running time: 0h1m36s