[2024-01-24 13:45:48,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:48,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:48,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference
[2024-01-24 13:45:50,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:50,110] [INFO] Task started: Prodigal
[2024-01-24 13:45:50,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg56cfd3b9-7572-4d74-bf91-0796cfaaad8b/GCF_000092925.1_ASM9292v1_genomic.fna.gz | prodigal -d GCF_000092925.1_ASM9292v1_genomic.fna/cds.fna -a GCF_000092925.1_ASM9292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:04,874] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:04,875] [INFO] Task started: HMMsearch
[2024-01-24 13:46:04,875] [INFO] Running command: hmmsearch --tblout GCF_000092925.1_ASM9292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference/reference_markers.hmm GCF_000092925.1_ASM9292v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:05,189] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:05,190] [INFO] Found 6/6 markers.
[2024-01-24 13:46:05,236] [INFO] Query marker FASTA was written to GCF_000092925.1_ASM9292v1_genomic.fna/markers.fasta
[2024-01-24 13:46:05,237] [INFO] Task started: Blastn
[2024-01-24 13:46:05,237] [INFO] Running command: blastn -query GCF_000092925.1_ASM9292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference/reference_markers.fasta -out GCF_000092925.1_ASM9292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:06,456] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:06,594] [INFO] Selected 10 target genomes.
[2024-01-24 13:46:06,594] [INFO] Target genome list was writen to GCF_000092925.1_ASM9292v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:06,600] [INFO] Task started: fastANI
[2024-01-24 13:46:06,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cfd3b9-7572-4d74-bf91-0796cfaaad8b/GCF_000092925.1_ASM9292v1_genomic.fna.gz --refList GCF_000092925.1_ASM9292v1_genomic.fna/target_genomes.txt --output GCF_000092925.1_ASM9292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:20,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:20,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:20,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:20,574] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:20,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:20,575] [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
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	100.0	1588	1588	95	conclusive
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	86.8561	1063	1588	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	85.7878	1051	1588	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	85.3294	1056	1588	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	84.8689	1041	1588	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	84.7159	1032	1588	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	84.5911	1042	1588	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	77.8394	443	1588	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.8222	599	1588	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	77.6242	437	1588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,576] [INFO] DFAST Taxonomy check result was written to GCF_000092925.1_ASM9292v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:20,577] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:20,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:20,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference/checkm_data
[2024-01-24 13:46:20,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:20,625] [INFO] Task started: CheckM
[2024-01-24 13:46:20,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092925.1_ASM9292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092925.1_ASM9292v1_genomic.fna/checkm_input GCF_000092925.1_ASM9292v1_genomic.fna/checkm_result
[2024-01-24 13:47:06,914] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:06,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,937] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:06,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:06,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092925.1_ASM9292v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:06,938] [INFO] Task started: Blastn
[2024-01-24 13:47:06,938] [INFO] Running command: blastn -query GCF_000092925.1_ASM9292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe4994a7-7df1-4490-8a2e-c8d968752d64/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092925.1_ASM9292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:09,309] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:09,319] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:09,319] [INFO] Target genome list was writen to GCF_000092925.1_ASM9292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:09,329] [INFO] Task started: fastANI
[2024-01-24 13:47:09,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cfd3b9-7572-4d74-bf91-0796cfaaad8b/GCF_000092925.1_ASM9292v1_genomic.fna.gz --refList GCF_000092925.1_ASM9292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092925.1_ASM9292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:21,459] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:21,471] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:21,472] [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_000092925.1	s__Starkeya novella	100.0	1588	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017872635.1	s__Starkeya sp017872635	92.7666	1277	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007559435.1	s__Starkeya sp007559435	87.35	1054	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_009223885.1	s__Ancylobacter sp009223885	86.9421	1040	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	85.7784	1054	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	85.3297	1056	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	84.8663	1042	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.7572	978	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241485.1	s__Angulomicrobium novellum_A	84.7042	950	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195655.1	s__Angulomicrobium tetraedrale	84.4749	991	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:21,473] [INFO] GTDB search result was written to GCF_000092925.1_ASM9292v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:21,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:21,477] [INFO] DFAST_QC result json was written to GCF_000092925.1_ASM9292v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:21,477] [INFO] DFAST_QC completed!
[2024-01-24 13:47:21,477] [INFO] Total running time: 0h1m33s