[2024-01-25 18:59:50,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference
[2024-01-25 18:59:51,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,907] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1171a2e-2407-4391-b078-54beda156bb9/GCF_003008595.1_ASM300859v1_genomic.fna.gz | prodigal -d GCF_003008595.1_ASM300859v1_genomic.fna/cds.fna -a GCF_003008595.1_ASM300859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:05,383] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:05,383] [INFO] Task started: HMMsearch
[2024-01-25 19:00:05,383] [INFO] Running command: hmmsearch --tblout GCF_003008595.1_ASM300859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference/reference_markers.hmm GCF_003008595.1_ASM300859v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:05,697] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:05,698] [INFO] Found 6/6 markers.
[2024-01-25 19:00:05,751] [INFO] Query marker FASTA was written to GCF_003008595.1_ASM300859v1_genomic.fna/markers.fasta
[2024-01-25 19:00:05,751] [INFO] Task started: Blastn
[2024-01-25 19:00:05,751] [INFO] Running command: blastn -query GCF_003008595.1_ASM300859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference/reference_markers.fasta -out GCF_003008595.1_ASM300859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:06,755] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:06,759] [INFO] Selected 18 target genomes.
[2024-01-25 19:00:06,759] [INFO] Target genome list was writen to GCF_003008595.1_ASM300859v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:06,766] [INFO] Task started: fastANI
[2024-01-25 19:00:06,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1171a2e-2407-4391-b078-54beda156bb9/GCF_003008595.1_ASM300859v1_genomic.fna.gz --refList GCF_003008595.1_ASM300859v1_genomic.fna/target_genomes.txt --output GCF_003008595.1_ASM300859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:24,301] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:24,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:24,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:24,313] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:24,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:24,313] [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
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	100.0	1381	1383	95	conclusive
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	84.8843	895	1383	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.8423	645	1383	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	80.7844	647	1383	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	80.3722	672	1383	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	80.279	568	1383	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.1203	613	1383	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.0943	675	1383	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	80.0548	564	1383	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	80.0045	669	1383	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	79.6821	526	1383	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	79.6369	364	1383	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	79.359	521	1383	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.2513	450	1383	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1977	458	1383	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.7059	465	1383	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.4999	418	1383	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.4307	461	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:24,315] [INFO] DFAST Taxonomy check result was written to GCF_003008595.1_ASM300859v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:24,315] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:24,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:24,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference/checkm_data
[2024-01-25 19:00:24,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:24,356] [INFO] Task started: CheckM
[2024-01-25 19:00:24,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003008595.1_ASM300859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003008595.1_ASM300859v1_genomic.fna/checkm_input GCF_003008595.1_ASM300859v1_genomic.fna/checkm_result
[2024-01-25 19:01:10,382] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:10,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:10,399] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:10,399] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:10,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003008595.1_ASM300859v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:10,400] [INFO] Task started: Blastn
[2024-01-25 19:01:10,400] [INFO] Running command: blastn -query GCF_003008595.1_ASM300859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51e28596-f2fd-457e-aacf-5d7f1a87ffde/dqc_reference/reference_markers_gtdb.fasta -out GCF_003008595.1_ASM300859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:12,208] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:12,213] [INFO] Selected 14 target genomes.
[2024-01-25 19:01:12,214] [INFO] Target genome list was writen to GCF_003008595.1_ASM300859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:12,228] [INFO] Task started: fastANI
[2024-01-25 19:01:12,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1171a2e-2407-4391-b078-54beda156bb9/GCF_003008595.1_ASM300859v1_genomic.fna.gz --refList GCF_003008595.1_ASM300859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003008595.1_ASM300859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:24,969] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:24,979] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:01:24,979] [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_003008595.1	s__Giesbergeria suum	100.0	1380	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017985015.1	s__Giesbergeria sp017985015	88.2322	900	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.01	95.86	0.92	0.90	6	-
GCF_003570885.1	s__Giesbergeria hankyongi	84.8503	899	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	82.4844	602	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096555.1	s__Giesbergeria sp003096555	81.8681	741	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCF_003604195.1	s__Giesbergeria lacusdiani	81.4967	714	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	81.3528	672	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCA_001770955.1	s__Giesbergeria sp001770955	81.003	663	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_000739995.1	s__Giesbergeria granuli	80.9176	671	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_010020825.1	s__Giesbergeria sp010020825	80.8576	692	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCF_014207955.1	s__Acidovorax soli_A	80.1524	695	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	80.0991	614	1383	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_003755025.1	s__Diaphorobacter nitroreducens	79.8693	589	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCF_000282995.1	s__Melaminivora alkalimesophila	79.6368	364	1383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:24,980] [INFO] GTDB search result was written to GCF_003008595.1_ASM300859v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:24,981] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:24,984] [INFO] DFAST_QC result json was written to GCF_003008595.1_ASM300859v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:24,984] [INFO] DFAST_QC completed!
[2024-01-25 19:01:24,984] [INFO] Total running time: 0h1m34s