[2023-06-28 18:14:23,958] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:14:23,965] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:14:23,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference
[2023-06-28 18:14:25,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:14:25,455] [INFO] Task started: Prodigal
[2023-06-28 18:14:25,455] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf58f21a-8d03-4bae-a370-865e3a523191/GCA_020442265.1_ASM2044226v1_genomic.fna.gz | prodigal -d GCA_020442265.1_ASM2044226v1_genomic.fna/cds.fna -a GCA_020442265.1_ASM2044226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:14:33,923] [INFO] Task succeeded: Prodigal
[2023-06-28 18:14:33,923] [INFO] Task started: HMMsearch
[2023-06-28 18:14:33,923] [INFO] Running command: hmmsearch --tblout GCA_020442265.1_ASM2044226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference/reference_markers.hmm GCA_020442265.1_ASM2044226v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:14:34,177] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:14:34,178] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbf58f21a-8d03-4bae-a370-865e3a523191/GCA_020442265.1_ASM2044226v1_genomic.fna.gz]
[2023-06-28 18:14:34,250] [INFO] Query marker FASTA was written to GCA_020442265.1_ASM2044226v1_genomic.fna/markers.fasta
[2023-06-28 18:14:34,250] [INFO] Task started: Blastn
[2023-06-28 18:14:34,250] [INFO] Running command: blastn -query GCA_020442265.1_ASM2044226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference/reference_markers.fasta -out GCA_020442265.1_ASM2044226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:14:34,922] [INFO] Task succeeded: Blastn
[2023-06-28 18:14:34,927] [INFO] Selected 26 target genomes.
[2023-06-28 18:14:34,927] [INFO] Target genome list was writen to GCA_020442265.1_ASM2044226v1_genomic.fna/target_genomes.txt
[2023-06-28 18:14:34,938] [INFO] Task started: fastANI
[2023-06-28 18:14:34,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf58f21a-8d03-4bae-a370-865e3a523191/GCA_020442265.1_ASM2044226v1_genomic.fna.gz --refList GCA_020442265.1_ASM2044226v1_genomic.fna/target_genomes.txt --output GCA_020442265.1_ASM2044226v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:14:54,182] [INFO] Task succeeded: fastANI
[2023-06-28 18:14:54,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:14:54,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:14:54,196] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:14:54,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:14:54,196] [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
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	76.5792	128	818	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	76.4801	121	818	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	76.3582	93	818	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	76.287	93	818	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	76.2511	91	818	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	76.1313	112	818	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	76.1239	89	818	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	76.061	101	818	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	76.0574	96	818	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	76.0092	107	818	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	75.9425	119	818	95	below_threshold
Pelagibacterium lentulum	strain=CGMCC 1.15896	GCA_014643755.1	2029865	2029865	type	True	75.8398	66	818	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	75.8274	67	818	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	75.7807	52	818	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.5575	73	818	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	75.4013	77	818	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:14:54,199] [INFO] DFAST Taxonomy check result was written to GCA_020442265.1_ASM2044226v1_genomic.fna/tc_result.tsv
[2023-06-28 18:14:54,200] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:14:54,200] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:14:54,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference/checkm_data
[2023-06-28 18:14:54,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:14:54,232] [INFO] Task started: CheckM
[2023-06-28 18:14:54,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020442265.1_ASM2044226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020442265.1_ASM2044226v1_genomic.fna/checkm_input GCA_020442265.1_ASM2044226v1_genomic.fna/checkm_result
[2023-06-28 18:15:23,073] [INFO] Task succeeded: CheckM
[2023-06-28 18:15:23,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.99%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:15:23,103] [INFO] ===== Completeness check finished =====
[2023-06-28 18:15:23,103] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:15:23,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020442265.1_ASM2044226v1_genomic.fna/markers.fasta)
[2023-06-28 18:15:23,104] [INFO] Task started: Blastn
[2023-06-28 18:15:23,104] [INFO] Running command: blastn -query GCA_020442265.1_ASM2044226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg929bca26-8012-453a-a046-79026356d8ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_020442265.1_ASM2044226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:15:24,032] [INFO] Task succeeded: Blastn
[2023-06-28 18:15:24,037] [INFO] Selected 25 target genomes.
[2023-06-28 18:15:24,038] [INFO] Target genome list was writen to GCA_020442265.1_ASM2044226v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:15:24,054] [INFO] Task started: fastANI
[2023-06-28 18:15:24,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf58f21a-8d03-4bae-a370-865e3a523191/GCA_020442265.1_ASM2044226v1_genomic.fna.gz --refList GCA_020442265.1_ASM2044226v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020442265.1_ASM2044226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:15:40,274] [INFO] Task succeeded: fastANI
[2023-06-28 18:15:40,292] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:15:40,292] [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
GCA_017794705.1	s__IH3 sp017794705	76.6365	166	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__IH3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411825.1	s__Devosia sp016411825	76.4801	121	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230555.1	s__Pelagibacterium halotolerans	76.3582	93	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002337455.1	s__Pelagibacterium sp002337455	76.3462	89	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCF_000970455.1	s__Devosia soli	76.287	93	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177655.1	s__Devosia lucknowensis	76.2707	90	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345525.1	s__Pelagibacterium lacus	76.1706	112	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375765.1	s__Pelagibacterium sp002375765	76.1057	99	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCF_003390885.1	s__Pelagibacterium sp003390885	76.061	101	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899085.1	s__Devosia_A sp001899085	76.0553	127	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_015158295.1	s__Devosia sp015158295	76.0092	107	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970465.2	s__Devosia_A insulae	75.9555	118	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	75.9457	68	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213505.1	s__Devosia_A nanyangense	75.9193	141	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425235.1	s__Devosia_A sp001425235	75.8792	111	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCF_014837245.1	s__Devosia sp014837245	75.8205	100	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824785.1	s__Mesorhizobium plurifarium	75.5954	71	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCF_002294725.1	s__Mesorhizobium sp002294725	75.4557	64	818	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.90	96.90	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-28 18:15:40,294] [INFO] GTDB search result was written to GCA_020442265.1_ASM2044226v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:15:40,295] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:15:40,299] [INFO] DFAST_QC result json was written to GCA_020442265.1_ASM2044226v1_genomic.fna/dqc_result.json
[2023-06-28 18:15:40,299] [INFO] DFAST_QC completed!
[2023-06-28 18:15:40,299] [INFO] Total running time: 0h1m16s