[2023-06-29 09:02:33,957] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:33,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:33,961] [INFO] DQC Reference Directory: /var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference
[2023-06-29 09:02:35,483] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:35,484] [INFO] Task started: Prodigal
[2023-06-29 09:02:35,484] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5ec0e8d-0bf2-4e9a-a24e-47f863a2211a/GCA_020697385.1_ASM2069738v1_genomic.fna.gz | prodigal -d GCA_020697385.1_ASM2069738v1_genomic.fna/cds.fna -a GCA_020697385.1_ASM2069738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:45,981] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:45,982] [INFO] Task started: HMMsearch
[2023-06-29 09:02:45,982] [INFO] Running command: hmmsearch --tblout GCA_020697385.1_ASM2069738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference/reference_markers.hmm GCA_020697385.1_ASM2069738v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:46,269] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:46,270] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5ec0e8d-0bf2-4e9a-a24e-47f863a2211a/GCA_020697385.1_ASM2069738v1_genomic.fna.gz]
[2023-06-29 09:02:46,309] [INFO] Query marker FASTA was written to GCA_020697385.1_ASM2069738v1_genomic.fna/markers.fasta
[2023-06-29 09:02:46,310] [INFO] Task started: Blastn
[2023-06-29 09:02:46,310] [INFO] Running command: blastn -query GCA_020697385.1_ASM2069738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference/reference_markers.fasta -out GCA_020697385.1_ASM2069738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:47,173] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:47,177] [INFO] Selected 20 target genomes.
[2023-06-29 09:02:47,178] [INFO] Target genome list was writen to GCA_020697385.1_ASM2069738v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:47,181] [INFO] Task started: fastANI
[2023-06-29 09:02:47,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ec0e8d-0bf2-4e9a-a24e-47f863a2211a/GCA_020697385.1_ASM2069738v1_genomic.fna.gz --refList GCA_020697385.1_ASM2069738v1_genomic.fna/target_genomes.txt --output GCA_020697385.1_ASM2069738v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:03:09,893] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:09,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:03:09,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:03:09,910] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:03:09,911] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:03:09,911] [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
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	90.3802	777	1097	95	below_threshold
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	88.1531	741	1097	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	87.8509	742	1097	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.3663	648	1097	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.3047	683	1097	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.0969	659	1097	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	83.7427	671	1097	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	82.4216	564	1097	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	81.9092	545	1097	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.4479	322	1097	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	78.2925	333	1097	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	77.138	107	1097	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.786	164	1097	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6352	162	1097	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.635	140	1097	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.6151	172	1097	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.6039	175	1097	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.4488	154	1097	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4448	155	1097	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.0794	104	1097	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:03:09,913] [INFO] DFAST Taxonomy check result was written to GCA_020697385.1_ASM2069738v1_genomic.fna/tc_result.tsv
[2023-06-29 09:03:09,914] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:03:09,914] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:03:09,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference/checkm_data
[2023-06-29 09:03:09,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:03:09,960] [INFO] Task started: CheckM
[2023-06-29 09:03:09,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020697385.1_ASM2069738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020697385.1_ASM2069738v1_genomic.fna/checkm_input GCA_020697385.1_ASM2069738v1_genomic.fna/checkm_result
[2023-06-29 09:03:45,446] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:45,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.35%
Contamintation: 18.98%
Strain heterogeneity: 23.08%
--------------------------------------------------------------------------------
[2023-06-29 09:03:45,478] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:45,478] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:45,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020697385.1_ASM2069738v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:45,479] [INFO] Task started: Blastn
[2023-06-29 09:03:45,479] [INFO] Running command: blastn -query GCA_020697385.1_ASM2069738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3948d980-3a11-4e92-abf3-51866ec56933/dqc_reference/reference_markers_gtdb.fasta -out GCA_020697385.1_ASM2069738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:46,956] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:46,963] [INFO] Selected 22 target genomes.
[2023-06-29 09:03:46,963] [INFO] Target genome list was writen to GCA_020697385.1_ASM2069738v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:46,975] [INFO] Task started: fastANI
[2023-06-29 09:03:46,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5ec0e8d-0bf2-4e9a-a24e-47f863a2211a/GCA_020697385.1_ASM2069738v1_genomic.fna.gz --refList GCA_020697385.1_ASM2069738v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020697385.1_ASM2069738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:04:09,740] [INFO] Task succeeded: fastANI
[2023-06-29 09:04:09,770] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:04:09,770] [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_016734765.1	s__Microvirga soli	90.3733	778	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739015.1	s__Microvirga sp000739015	88.6453	731	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699075.1	s__Microvirga sp014699075	88.3751	772	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811235.1	s__Microvirga arabica	88.1716	740	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191055.1	s__Microvirga lupini_A	88.0576	737	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694425.1	s__Microvirga sp015694425	88.0337	720	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427565.1	s__Microvirga sp016427565	87.8509	742	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892765.1	s__Microvirga sp016892765	85.9629	729	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743775.1	s__Microvirga aerilata	84.3817	647	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741015.1	s__Microvirga ossetica	84.3157	682	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735695.1	s__Microvirga zambiensis	84.0784	660	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069605.1	s__Microvirga sp018069605	83.6696	666	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	77.2488	128	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	77.0869	157	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	76.9633	133	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	76.9045	153	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	76.7865	165	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	76.4542	183	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	76.4229	156	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.3913	98	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_902826935.1	s__CADEGR01 sp902826935	75.8242	112	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-29 09:04:09,772] [INFO] GTDB search result was written to GCA_020697385.1_ASM2069738v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:04:09,773] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:04:09,778] [INFO] DFAST_QC result json was written to GCA_020697385.1_ASM2069738v1_genomic.fna/dqc_result.json
[2023-06-29 09:04:09,778] [INFO] DFAST_QC completed!
[2023-06-29 09:04:09,778] [INFO] Total running time: 0h1m36s