[2024-01-24 13:09:33,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference
[2024-01-24 13:09:35,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,256] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,256] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0cca4a1-feb6-4b31-a860-fa8ea175f1ca/GCF_007559435.1_ASM755943v1_genomic.fna.gz | prodigal -d GCF_007559435.1_ASM755943v1_genomic.fna/cds.fna -a GCF_007559435.1_ASM755943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:47,264] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:47,264] [INFO] Task started: HMMsearch
[2024-01-24 13:09:47,264] [INFO] Running command: hmmsearch --tblout GCF_007559435.1_ASM755943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference/reference_markers.hmm GCF_007559435.1_ASM755943v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:47,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:47,545] [INFO] Found 6/6 markers.
[2024-01-24 13:09:47,580] [INFO] Query marker FASTA was written to GCF_007559435.1_ASM755943v1_genomic.fna/markers.fasta
[2024-01-24 13:09:47,580] [INFO] Task started: Blastn
[2024-01-24 13:09:47,580] [INFO] Running command: blastn -query GCF_007559435.1_ASM755943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference/reference_markers.fasta -out GCF_007559435.1_ASM755943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:48,805] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:48,809] [INFO] Selected 11 target genomes.
[2024-01-24 13:09:48,809] [INFO] Target genome list was writen to GCF_007559435.1_ASM755943v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:48,814] [INFO] Task started: fastANI
[2024-01-24 13:09:48,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0cca4a1-feb6-4b31-a860-fa8ea175f1ca/GCF_007559435.1_ASM755943v1_genomic.fna.gz --refList GCF_007559435.1_ASM755943v1_genomic.fna/target_genomes.txt --output GCF_007559435.1_ASM755943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:02,160] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:02,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:02,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:02,171] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:02,171] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:02,171] [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	87.4181	1041	1387	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	86.7309	989	1387	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	85.7414	967	1387	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	85.3476	945	1387	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	85.0459	960	1387	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	84.2767	931	1387	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	84.0896	975	1387	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	83.669	915	1387	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	78.1222	448	1387	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.9986	428	1387	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.7812	515	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:02,173] [INFO] DFAST Taxonomy check result was written to GCF_007559435.1_ASM755943v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:02,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:02,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:02,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference/checkm_data
[2024-01-24 13:10:02,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:02,213] [INFO] Task started: CheckM
[2024-01-24 13:10:02,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007559435.1_ASM755943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007559435.1_ASM755943v1_genomic.fna/checkm_input GCF_007559435.1_ASM755943v1_genomic.fna/checkm_result
[2024-01-24 13:10:39,531] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:39,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:39,549] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:39,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:39,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007559435.1_ASM755943v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:39,550] [INFO] Task started: Blastn
[2024-01-24 13:10:39,550] [INFO] Running command: blastn -query GCF_007559435.1_ASM755943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155000d4-a09b-4857-b2aa-1e23e8736b67/dqc_reference/reference_markers_gtdb.fasta -out GCF_007559435.1_ASM755943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:41,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:41,782] [INFO] Selected 11 target genomes.
[2024-01-24 13:10:41,782] [INFO] Target genome list was writen to GCF_007559435.1_ASM755943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:41,789] [INFO] Task started: fastANI
[2024-01-24 13:10:41,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0cca4a1-feb6-4b31-a860-fa8ea175f1ca/GCF_007559435.1_ASM755943v1_genomic.fna.gz --refList GCF_007559435.1_ASM755943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007559435.1_ASM755943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:53,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:53,518] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:53,518] [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_007559435.1	s__Starkeya sp007559435	100.0	1387	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	conclusive
GCF_000092925.1	s__Starkeya novella	87.4214	1041	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	87.379	1029	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009223885.1	s__Ancylobacter sp009223885	86.9099	996	1387	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	85.7531	966	1387	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	85.3361	946	1387	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	85.0806	956	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241485.1	s__Angulomicrobium novellum_A	84.6889	894	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.3697	948	1387	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	84.3481	925	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	84.1833	938	1387	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:53,520] [INFO] GTDB search result was written to GCF_007559435.1_ASM755943v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:53,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:53,524] [INFO] DFAST_QC result json was written to GCF_007559435.1_ASM755943v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:53,525] [INFO] DFAST_QC completed!
[2024-01-24 13:10:53,525] [INFO] Total running time: 0h1m20s