[2024-01-24 12:53:56,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference
[2024-01-24 12:53:57,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:57,919] [INFO] Task started: Prodigal
[2024-01-24 12:53:57,920] [INFO] Running command: gunzip -c /var/lib/cwl/stgc400042b-0eb7-4ba8-80b9-e2a1e8c63184/GCF_007655255.1_ASM765525v1_genomic.fna.gz | prodigal -d GCF_007655255.1_ASM765525v1_genomic.fna/cds.fna -a GCF_007655255.1_ASM765525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:10,463] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:10,463] [INFO] Task started: HMMsearch
[2024-01-24 12:54:10,463] [INFO] Running command: hmmsearch --tblout GCF_007655255.1_ASM765525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference/reference_markers.hmm GCF_007655255.1_ASM765525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:10,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:10,705] [INFO] Found 6/6 markers.
[2024-01-24 12:54:10,739] [INFO] Query marker FASTA was written to GCF_007655255.1_ASM765525v1_genomic.fna/markers.fasta
[2024-01-24 12:54:10,740] [INFO] Task started: Blastn
[2024-01-24 12:54:10,740] [INFO] Running command: blastn -query GCF_007655255.1_ASM765525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference/reference_markers.fasta -out GCF_007655255.1_ASM765525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:11,674] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:11,678] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:11,679] [INFO] Target genome list was writen to GCF_007655255.1_ASM765525v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:11,686] [INFO] Task started: fastANI
[2024-01-24 12:54:11,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgc400042b-0eb7-4ba8-80b9-e2a1e8c63184/GCF_007655255.1_ASM765525v1_genomic.fna.gz --refList GCF_007655255.1_ASM765525v1_genomic.fna/target_genomes.txt --output GCF_007655255.1_ASM765525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:25,816] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:25,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:25,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:25,833] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:25,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:25,833] [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
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	100.0	1151	1169	95	conclusive
Extensimonas vulgaris	strain=CGMCC 1.10977	GCA_007830535.1	1031594	1031594	type	True	91.3117	813	1169	95	below_threshold
Extensimonas vulgaris	strain=S4	GCA_007996985.1	1031594	1031594	type	True	91.2518	805	1169	95	below_threshold
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	91.2337	808	1169	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.7294	595	1169	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.4392	580	1169	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.2802	535	1169	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	80.0897	567	1169	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	79.9084	477	1169	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	79.8552	571	1169	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	79.4412	475	1169	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.3978	460	1169	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.049	466	1169	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.7591	463	1169	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.4216	355	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:25,835] [INFO] DFAST Taxonomy check result was written to GCF_007655255.1_ASM765525v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:25,836] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:25,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:25,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference/checkm_data
[2024-01-24 12:54:25,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:25,876] [INFO] Task started: CheckM
[2024-01-24 12:54:25,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007655255.1_ASM765525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007655255.1_ASM765525v1_genomic.fna/checkm_input GCF_007655255.1_ASM765525v1_genomic.fna/checkm_result
[2024-01-24 12:55:04,869] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:04,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:04,889] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:04,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:04,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007655255.1_ASM765525v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:04,890] [INFO] Task started: Blastn
[2024-01-24 12:55:04,891] [INFO] Running command: blastn -query GCF_007655255.1_ASM765525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21838319-49f8-4bce-91cd-a6e7072f3cb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007655255.1_ASM765525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:06,680] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:06,683] [INFO] Selected 18 target genomes.
[2024-01-24 12:55:06,683] [INFO] Target genome list was writen to GCF_007655255.1_ASM765525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:06,695] [INFO] Task started: fastANI
[2024-01-24 12:55:06,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgc400042b-0eb7-4ba8-80b9-e2a1e8c63184/GCF_007655255.1_ASM765525v1_genomic.fna.gz --refList GCF_007655255.1_ASM765525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007655255.1_ASM765525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:22,728] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:22,744] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:22,744] [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_007655255.1	s__Extensimonas perlucida	100.0	1150	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	97.84	97.67	0.89	0.88	3	conclusive
GCF_003337425.1	s__Extensimonas vulgaris	91.2336	808	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Extensimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003604195.1	s__Giesbergeria lacusdiani	81.1311	573	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	81.0354	590	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_002176815.1	s__Acidovorax sp002176815	81.0018	583	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCF_000400995.2	s__MR-S7 sp000400995	80.8308	612	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_003269065.1	s__Acidovorax_A anthurii	80.429	581	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770955.1	s__Giesbergeria sp001770955	80.3284	509	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_014207955.1	s__Acidovorax soli_A	80.3268	625	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408765.1	s__Acidovorax sp013408765	80.2581	592	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001714725.1	s__Acidovorax sp001714725	80.0937	522	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693755.1	s__Tibeticola sp013693755	80.0338	494	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tibeticola	95.0	96.98	96.98	0.89	0.89	2	-
GCA_001724785.1	s__Giesbergeria sp001724785	79.9815	417	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556755.1	s__Tepidimonas fonticaldi	79.7253	426	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	97.94	97.94	0.88	0.88	2	-
GCF_000463015.1	s__Variovorax paradoxus_E	79.3624	506	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	98.39	98.39	0.87	0.87	2	-
GCF_007556705.1	s__Tepidimonas thermarum	79.2151	379	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464865.1	s__Acidovorax sp001464865	78.9817	451	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013432195.1	s__Tepidicella baoligensis	78.925	338	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:22,747] [INFO] GTDB search result was written to GCF_007655255.1_ASM765525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:22,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:22,752] [INFO] DFAST_QC result json was written to GCF_007655255.1_ASM765525v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:22,752] [INFO] DFAST_QC completed!
[2024-01-24 12:55:22,752] [INFO] Total running time: 0h1m26s