[2024-01-25 20:11:50,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:50,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:50,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference
[2024-01-25 20:11:51,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:51,755] [INFO] Task started: Prodigal
[2024-01-25 20:11:51,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg4573040a-6fad-4153-8b4c-8467197217ef/GCF_009763355.1_ASM976335v1_genomic.fna.gz | prodigal -d GCF_009763355.1_ASM976335v1_genomic.fna/cds.fna -a GCF_009763355.1_ASM976335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:11,514] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:11,515] [INFO] Task started: HMMsearch
[2024-01-25 20:12:11,515] [INFO] Running command: hmmsearch --tblout GCF_009763355.1_ASM976335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference/reference_markers.hmm GCF_009763355.1_ASM976335v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:11,803] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:11,804] [INFO] Found 6/6 markers.
[2024-01-25 20:12:11,859] [INFO] Query marker FASTA was written to GCF_009763355.1_ASM976335v1_genomic.fna/markers.fasta
[2024-01-25 20:12:11,859] [INFO] Task started: Blastn
[2024-01-25 20:12:11,859] [INFO] Running command: blastn -query GCF_009763355.1_ASM976335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference/reference_markers.fasta -out GCF_009763355.1_ASM976335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:12,680] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:12,683] [INFO] Selected 14 target genomes.
[2024-01-25 20:12:12,683] [INFO] Target genome list was writen to GCF_009763355.1_ASM976335v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:12,693] [INFO] Task started: fastANI
[2024-01-25 20:12:12,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg4573040a-6fad-4153-8b4c-8467197217ef/GCF_009763355.1_ASM976335v1_genomic.fna.gz --refList GCF_009763355.1_ASM976335v1_genomic.fna/target_genomes.txt --output GCF_009763355.1_ASM976335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:32,722] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:32,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:32,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:32,733] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:32,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:32,734] [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
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	89.9796	1770	2432	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	89.4659	1787	2432	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	89.0661	1721	2432	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.955	1366	2432	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	83.5265	1427	2432	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	82.1433	1205	2432	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	81.8595	1184	2432	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.7897	1101	2432	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.6567	1149	2432	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	76.9263	479	2432	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.7535	372	2432	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	76.1048	273	2432	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	76.0752	239	2432	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	75.612	255	2432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:32,735] [INFO] DFAST Taxonomy check result was written to GCF_009763355.1_ASM976335v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:32,736] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:32,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:32,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference/checkm_data
[2024-01-25 20:12:32,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:32,803] [INFO] Task started: CheckM
[2024-01-25 20:12:32,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009763355.1_ASM976335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009763355.1_ASM976335v1_genomic.fna/checkm_input GCF_009763355.1_ASM976335v1_genomic.fna/checkm_result
[2024-01-25 20:13:40,548] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:40,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:40,579] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:40,579] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:40,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009763355.1_ASM976335v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:40,580] [INFO] Task started: Blastn
[2024-01-25 20:13:40,580] [INFO] Running command: blastn -query GCF_009763355.1_ASM976335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21b69c42-b3d4-4bcb-baa4-6ef5fcf41126/dqc_reference/reference_markers_gtdb.fasta -out GCF_009763355.1_ASM976335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:42,128] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:42,132] [INFO] Selected 13 target genomes.
[2024-01-25 20:13:42,132] [INFO] Target genome list was writen to GCF_009763355.1_ASM976335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:42,143] [INFO] Task started: fastANI
[2024-01-25 20:13:42,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg4573040a-6fad-4153-8b4c-8467197217ef/GCF_009763355.1_ASM976335v1_genomic.fna.gz --refList GCF_009763355.1_ASM976335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009763355.1_ASM976335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:03,676] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:03,688] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:03,688] [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_001426525.1	s__Massilia sp001426525	99.3818	2238	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.62	99.38	0.97	0.95	3	conclusive
GCF_000759615.1	s__Massilia sp000759615	93.2493	2032	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101265.1	s__Massilia sp900101265	92.8931	2042	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968015.1	s__Massilia phosphatilytica	92.5541	1999	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941825.1	s__Massilia putida	89.9764	1770	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425685.1	s__Massilia sp001425685	89.7362	1798	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016093545.1	s__Massilia sp016093545	89.4719	1786	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682055.1	s__Massilia sp011682055	88.9591	1773	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424165.1	s__Massilia sp001424165	81.7195	1090	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289985.1	s__CAIMXF01 sp013289985	76.9854	544	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIMXF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722765.1	s__Ramlibacter alkalitolerans	76.9322	477	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	76.7934	366	2432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:03,690] [INFO] GTDB search result was written to GCF_009763355.1_ASM976335v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:03,690] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:03,693] [INFO] DFAST_QC result json was written to GCF_009763355.1_ASM976335v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:03,693] [INFO] DFAST_QC completed!
[2024-01-25 20:14:03,693] [INFO] Total running time: 0h2m13s