[2024-01-25 18:40:35,769] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:35,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:35,771] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference
[2024-01-25 18:40:36,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:36,898] [INFO] Task started: Prodigal
[2024-01-25 18:40:36,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgff29c6c9-37b6-4f89-b249-f43f53ffd8fe/GCF_003590875.1_ASM359087v1_genomic.fna.gz | prodigal -d GCF_003590875.1_ASM359087v1_genomic.fna/cds.fna -a GCF_003590875.1_ASM359087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:51,740] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:51,741] [INFO] Task started: HMMsearch
[2024-01-25 18:40:51,741] [INFO] Running command: hmmsearch --tblout GCF_003590875.1_ASM359087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference/reference_markers.hmm GCF_003590875.1_ASM359087v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:52,023] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:52,024] [INFO] Found 6/6 markers.
[2024-01-25 18:40:52,068] [INFO] Query marker FASTA was written to GCF_003590875.1_ASM359087v1_genomic.fna/markers.fasta
[2024-01-25 18:40:52,068] [INFO] Task started: Blastn
[2024-01-25 18:40:52,068] [INFO] Running command: blastn -query GCF_003590875.1_ASM359087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference/reference_markers.fasta -out GCF_003590875.1_ASM359087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:52,922] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:52,925] [INFO] Selected 19 target genomes.
[2024-01-25 18:40:52,925] [INFO] Target genome list was writen to GCF_003590875.1_ASM359087v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:52,934] [INFO] Task started: fastANI
[2024-01-25 18:40:52,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgff29c6c9-37b6-4f89-b249-f43f53ffd8fe/GCF_003590875.1_ASM359087v1_genomic.fna.gz --refList GCF_003590875.1_ASM359087v1_genomic.fna/target_genomes.txt --output GCF_003590875.1_ASM359087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:13,744] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:13,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:13,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:13,756] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:13,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:13,756] [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
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	100.0	1551	1553	95	conclusive
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	80.1838	650	1553	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	80.1495	602	1553	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.9458	611	1553	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	79.8516	603	1553	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	79.7471	551	1553	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	79.5895	559	1553	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	79.5757	569	1553	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	79.5568	528	1553	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.3842	404	1553	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.247	395	1553	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	79.2266	444	1553	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	78.9518	482	1553	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	78.8457	439	1553	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	78.6377	435	1553	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	78.6365	407	1553	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	78.5882	411	1553	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	78.3978	382	1553	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	78.2585	369	1553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:13,760] [INFO] DFAST Taxonomy check result was written to GCF_003590875.1_ASM359087v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:13,761] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:13,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:13,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference/checkm_data
[2024-01-25 18:41:13,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:13,827] [INFO] Task started: CheckM
[2024-01-25 18:41:13,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590875.1_ASM359087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590875.1_ASM359087v1_genomic.fna/checkm_input GCF_003590875.1_ASM359087v1_genomic.fna/checkm_result
[2024-01-25 18:42:15,255] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:15,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:15,275] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:15,275] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:15,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590875.1_ASM359087v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:15,276] [INFO] Task started: Blastn
[2024-01-25 18:42:15,276] [INFO] Running command: blastn -query GCF_003590875.1_ASM359087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8bae5ef-0bc8-4002-8aaf-8a609b615258/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590875.1_ASM359087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:16,966] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:16,971] [INFO] Selected 20 target genomes.
[2024-01-25 18:42:16,971] [INFO] Target genome list was writen to GCF_003590875.1_ASM359087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:16,983] [INFO] Task started: fastANI
[2024-01-25 18:42:16,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgff29c6c9-37b6-4f89-b249-f43f53ffd8fe/GCF_003590875.1_ASM359087v1_genomic.fna.gz --refList GCF_003590875.1_ASM359087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590875.1_ASM359087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:37,664] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:37,676] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:37,677] [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_003590875.1	s__Noviherbaspirillum sp003590875	100.0	1549	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007874125.1	s__Noviherbaspirillum sp007874125	80.4734	644	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	80.2052	646	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	80.0926	607	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008929045.1	s__Noviherbaspirillum aerium	79.9586	615	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211445.1	s__Noviherbaspirillum denitrificans	79.8416	607	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	79.7208	555	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804275.1	s__Noviherbaspirillum sp004804275	79.6535	585	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974945.1	s__Noviherbaspirillum galbum	79.5589	571	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312045.1	s__Noviherbaspirillum massiliense	79.5472	529	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000221045.1	s__Collimonas fungivorans_A	79.3041	428	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	79.2811	389	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267925.1	s__Herbaspirillum hiltneri	79.2438	446	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.60	97.60	0.89	0.89	2	-
GCF_006715495.1	s__Herbaspirillum sp006715495	79.2353	453	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.71	99.15	0.99	0.96	4	-
GCF_001428545.1	s__Noviherbaspirillum sp001428545	79.2278	493	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114795.1	s__Paucimonas sp004114795	78.995	404	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112135.1	s__Collimonas sp900112135	78.8893	428	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCA_019232795.1	s__PKWO01 sp019232795	78.619	300	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PKWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	78.6061	435	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_018305005.1	s__Collimonas sp018305005	78.262	369	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:37,680] [INFO] GTDB search result was written to GCF_003590875.1_ASM359087v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:37,681] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:37,685] [INFO] DFAST_QC result json was written to GCF_003590875.1_ASM359087v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:37,685] [INFO] DFAST_QC completed!
[2024-01-25 18:42:37,685] [INFO] Total running time: 0h2m2s