[2024-01-24 13:31:44,330] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference
[2024-01-24 13:31:45,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,592] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg951c7b33-d80a-4e72-b3cf-2e5c839cfd2c/GCF_014642815.1_ASM1464281v1_genomic.fna.gz | prodigal -d GCF_014642815.1_ASM1464281v1_genomic.fna/cds.fna -a GCF_014642815.1_ASM1464281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:02,205] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:02,206] [INFO] Task started: HMMsearch
[2024-01-24 13:32:02,206] [INFO] Running command: hmmsearch --tblout GCF_014642815.1_ASM1464281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference/reference_markers.hmm GCF_014642815.1_ASM1464281v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:02,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:02,519] [INFO] Found 6/6 markers.
[2024-01-24 13:32:02,567] [INFO] Query marker FASTA was written to GCF_014642815.1_ASM1464281v1_genomic.fna/markers.fasta
[2024-01-24 13:32:02,567] [INFO] Task started: Blastn
[2024-01-24 13:32:02,567] [INFO] Running command: blastn -query GCF_014642815.1_ASM1464281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference/reference_markers.fasta -out GCF_014642815.1_ASM1464281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:03,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:03,406] [INFO] Selected 14 target genomes.
[2024-01-24 13:32:03,406] [INFO] Target genome list was writen to GCF_014642815.1_ASM1464281v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:03,415] [INFO] Task started: fastANI
[2024-01-24 13:32:03,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg951c7b33-d80a-4e72-b3cf-2e5c839cfd2c/GCF_014642815.1_ASM1464281v1_genomic.fna.gz --refList GCF_014642815.1_ASM1464281v1_genomic.fna/target_genomes.txt --output GCF_014642815.1_ASM1464281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:16,847] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:16,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:16,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:16,860] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:16,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:16,861] [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
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	100.0	1600	1602	95	conclusive
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	99.9992	1600	1602	95	conclusive
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	82.9936	1038	1602	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	82.8778	970	1602	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	82.2215	940	1602	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	81.4837	857	1602	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	80.7263	795	1602	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	80.6897	783	1602	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.5956	488	1602	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.5339	574	1602	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.1982	456	1602	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.9493	166	1602	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	77.7256	209	1602	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	77.7212	204	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,862] [INFO] DFAST Taxonomy check result was written to GCF_014642815.1_ASM1464281v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:16,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:16,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:16,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference/checkm_data
[2024-01-24 13:32:16,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:16,916] [INFO] Task started: CheckM
[2024-01-24 13:32:16,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642815.1_ASM1464281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642815.1_ASM1464281v1_genomic.fna/checkm_input GCF_014642815.1_ASM1464281v1_genomic.fna/checkm_result
[2024-01-24 13:33:06,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:06,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,891] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:06,891] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:06,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642815.1_ASM1464281v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:06,892] [INFO] Task started: Blastn
[2024-01-24 13:33:06,892] [INFO] Running command: blastn -query GCF_014642815.1_ASM1464281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeea5e9a3-abe1-46e1-9773-d9cad249478a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642815.1_ASM1464281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:08,134] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:08,138] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:08,139] [INFO] Target genome list was writen to GCF_014642815.1_ASM1464281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:08,156] [INFO] Task started: fastANI
[2024-01-24 13:33:08,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg951c7b33-d80a-4e72-b3cf-2e5c839cfd2c/GCF_014642815.1_ASM1464281v1_genomic.fna.gz --refList GCF_014642815.1_ASM1464281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642815.1_ASM1464281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:24,095] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:24,109] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:24,109] [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_016865235.1	s__Dyella_B caseinilytica	99.9992	1601	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014863405.1	s__Dyella_B sp014863405	82.9876	1039	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904955.1	s__Dyella_B flava	82.8778	970	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	82.2246	940	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363265.1	s__Dyella_B psychrodurans	81.4971	855	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970555.1	s__Dyella_B sp903970555	81.0873	735	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873315.1	s__Dyella_B sp014873315	80.8058	827	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363155.1	s__Dyella_B monticola	80.7342	794	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977665.1	s__Dyella_B choica	80.6967	781	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	79.8482	604	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_900112865.1	s__Dyella marensis	79.6362	602	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014842975.1	s__Rhodanobacter sp014842975	79.6347	535	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	79.5864	571	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	77.7256	209	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:24,112] [INFO] GTDB search result was written to GCF_014642815.1_ASM1464281v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:24,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:24,117] [INFO] DFAST_QC result json was written to GCF_014642815.1_ASM1464281v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:24,117] [INFO] DFAST_QC completed!
[2024-01-24 13:33:24,118] [INFO] Total running time: 0h1m40s