[2024-01-25 18:37:20,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:20,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:20,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference
[2024-01-25 18:37:21,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:21,665] [INFO] Task started: Prodigal
[2024-01-25 18:37:21,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a0c880c-a7be-4efe-bf60-6dbe3909dafe/GCF_030814655.1_ASM3081465v1_genomic.fna.gz | prodigal -d GCF_030814655.1_ASM3081465v1_genomic.fna/cds.fna -a GCF_030814655.1_ASM3081465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:40,406] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:40,407] [INFO] Task started: HMMsearch
[2024-01-25 18:37:40,407] [INFO] Running command: hmmsearch --tblout GCF_030814655.1_ASM3081465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference/reference_markers.hmm GCF_030814655.1_ASM3081465v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:40,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:40,688] [INFO] Found 6/6 markers.
[2024-01-25 18:37:40,740] [INFO] Query marker FASTA was written to GCF_030814655.1_ASM3081465v1_genomic.fna/markers.fasta
[2024-01-25 18:37:40,740] [INFO] Task started: Blastn
[2024-01-25 18:37:40,741] [INFO] Running command: blastn -query GCF_030814655.1_ASM3081465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference/reference_markers.fasta -out GCF_030814655.1_ASM3081465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:41,732] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:41,736] [INFO] Selected 32 target genomes.
[2024-01-25 18:37:41,736] [INFO] Target genome list was writen to GCF_030814655.1_ASM3081465v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:41,754] [INFO] Task started: fastANI
[2024-01-25 18:37:41,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a0c880c-a7be-4efe-bf60-6dbe3909dafe/GCF_030814655.1_ASM3081465v1_genomic.fna.gz --refList GCF_030814655.1_ASM3081465v1_genomic.fna/target_genomes.txt --output GCF_030814655.1_ASM3081465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:38:15,375] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:15,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:38:15,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:38:15,395] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:38:15,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:38:15,395] [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
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.9168	488	2306	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.8708	507	2306	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.7852	523	2306	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.7329	483	2306	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.729	369	2306	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.695	505	2306	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.6866	485	2306	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.6326	465	2306	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	77.606	362	2306	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	77.5846	502	2306	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.5571	543	2306	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	77.5464	369	2306	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	77.5059	337	2306	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	77.505	505	2306	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.4607	592	2306	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.33	456	2306	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	77.3184	438	2306	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.2976	463	2306	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.2793	333	2306	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	77.2625	501	2306	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.2352	417	2306	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	77.2349	515	2306	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.2073	471	2306	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	77.1879	396	2306	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	77.1801	528	2306	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.0871	448	2306	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	77.0709	387	2306	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.0457	582	2306	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	77.0299	370	2306	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.9789	558	2306	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.9587	542	2306	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	76.6992	327	2306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:38:15,396] [INFO] DFAST Taxonomy check result was written to GCF_030814655.1_ASM3081465v1_genomic.fna/tc_result.tsv
[2024-01-25 18:38:15,397] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:38:15,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:38:15,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference/checkm_data
[2024-01-25 18:38:15,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:38:15,471] [INFO] Task started: CheckM
[2024-01-25 18:38:15,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814655.1_ASM3081465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814655.1_ASM3081465v1_genomic.fna/checkm_input GCF_030814655.1_ASM3081465v1_genomic.fna/checkm_result
[2024-01-25 18:39:34,141] [INFO] Task succeeded: CheckM
[2024-01-25 18:39:34,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:39:34,163] [INFO] ===== Completeness check finished =====
[2024-01-25 18:39:34,164] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:39:34,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814655.1_ASM3081465v1_genomic.fna/markers.fasta)
[2024-01-25 18:39:34,164] [INFO] Task started: Blastn
[2024-01-25 18:39:34,164] [INFO] Running command: blastn -query GCF_030814655.1_ASM3081465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7542cdf1-1c96-4e55-be61-cfd68e930f4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814655.1_ASM3081465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:36,257] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:36,260] [INFO] Selected 18 target genomes.
[2024-01-25 18:39:36,260] [INFO] Target genome list was writen to GCF_030814655.1_ASM3081465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:39:36,295] [INFO] Task started: fastANI
[2024-01-25 18:39:36,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a0c880c-a7be-4efe-bf60-6dbe3909dafe/GCF_030814655.1_ASM3081465v1_genomic.fna.gz --refList GCF_030814655.1_ASM3081465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814655.1_ASM3081465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:39:56,364] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:56,375] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:39:56,376] [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_002982075.1	s__Labrys okinawensis	81.0615	1003	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	98.61	98.61	0.96	0.96	2	-
GCF_001676615.1	s__Labrys sp001676615	80.9188	1006	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008330945.1	s__Labrys sp008330945	80.8012	1020	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390635.1	s__Ancylobacter_C lacus	78.3434	545	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	77.8503	565	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.7694	524	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_900168195.1	s__Bosea thiooxidans	77.707	503	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCA_900466745.1	s__Bosea sp900466745	77.6652	562	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_900102525.1	s__Bosea robiniae	77.649	490	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCF_017875275.1	s__Xanthobacter flavus	77.5498	434	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	77.5093	503	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298265.1	s__Bosea vaviloviae_B	77.4127	475	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176205.1	s__Bradyrhizobium sp900176205	77.3644	489	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003046185.1	s__Phreatobacter oligotrophus	77.3504	454	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248805.1	s__Bosea sp003248805	77.2055	479	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305455.1	s__Afipia sp017305455	77.1547	294	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304475.1	s__Phreatobacter sp017304475	77.1433	606	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	77.1124	412	2306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:39:56,377] [INFO] GTDB search result was written to GCF_030814655.1_ASM3081465v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:39:56,377] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:39:56,381] [INFO] DFAST_QC result json was written to GCF_030814655.1_ASM3081465v1_genomic.fna/dqc_result.json
[2024-01-25 18:39:56,382] [INFO] DFAST_QC completed!
[2024-01-25 18:39:56,382] [INFO] Total running time: 0h2m36s