[2024-01-25 18:47:20,511] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:20,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:20,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference
[2024-01-25 18:47:21,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:21,652] [INFO] Task started: Prodigal
[2024-01-25 18:47:21,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b962423-7300-430b-aeb0-f3ceda91a763/GCF_000466945.1_ASM46694v1_genomic.fna.gz | prodigal -d GCF_000466945.1_ASM46694v1_genomic.fna/cds.fna -a GCF_000466945.1_ASM46694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:33,669] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:33,670] [INFO] Task started: HMMsearch
[2024-01-25 18:47:33,670] [INFO] Running command: hmmsearch --tblout GCF_000466945.1_ASM46694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference/reference_markers.hmm GCF_000466945.1_ASM46694v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:33,961] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:33,962] [INFO] Found 6/6 markers.
[2024-01-25 18:47:34,005] [INFO] Query marker FASTA was written to GCF_000466945.1_ASM46694v1_genomic.fna/markers.fasta
[2024-01-25 18:47:34,005] [INFO] Task started: Blastn
[2024-01-25 18:47:34,006] [INFO] Running command: blastn -query GCF_000466945.1_ASM46694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference/reference_markers.fasta -out GCF_000466945.1_ASM46694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:34,818] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:34,821] [INFO] Selected 24 target genomes.
[2024-01-25 18:47:34,822] [INFO] Target genome list was writen to GCF_000466945.1_ASM46694v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:34,857] [INFO] Task started: fastANI
[2024-01-25 18:47:34,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b962423-7300-430b-aeb0-f3ceda91a763/GCF_000466945.1_ASM46694v1_genomic.fna.gz --refList GCF_000466945.1_ASM46694v1_genomic.fna/target_genomes.txt --output GCF_000466945.1_ASM46694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:50,753] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:50,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:50,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:50,768] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:47:50,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:50,768] [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
Caenibius tardaugens	strain=NBRC 16725	GCA_000466945.1	169176	169176	type	True	100.0	1403	1406	95	conclusive
Caenibius tardaugens	strain=NBRC 16725	GCA_003860345.1	169176	169176	type	True	99.9981	1406	1406	95	conclusive
Novosphingobium olei	strain=TW-4	GCA_012927405.1	2728851	2728851	type	True	78.3187	293	1406	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.2481	322	1406	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.1281	266	1406	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.0367	249	1406	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	78.0002	281	1406	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	77.8943	256	1406	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.8934	253	1406	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.8625	233	1406	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	77.8357	251	1406	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.8211	204	1406	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	77.8143	236	1406	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	77.7839	192	1406	95	below_threshold
Novosphingobium subterraneum	strain=NBRC 16086	GCA_001598575.1	48936	48936	type	True	77.7822	273	1406	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	77.7801	253	1406	95	below_threshold
Novosphingobium colocasiae	strain=KCTC 32255	GCA_014652555.1	1256513	1256513	type	True	77.7753	302	1406	95	below_threshold
Qipengyuania pacifica	strain=NZ-96	GCA_019857205.1	2860199	2860199	type	True	77.77	217	1406	95	below_threshold
Novosphingobium subterraneum	strain=DSM 12447	GCA_000807925.1	48936	48936	type	True	77.7665	281	1406	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7085	203	1406	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	77.7077	247	1406	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.6192	296	1406	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	77.5767	207	1406	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	77.4895	204	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:50,770] [INFO] DFAST Taxonomy check result was written to GCF_000466945.1_ASM46694v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:50,770] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:50,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:50,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference/checkm_data
[2024-01-25 18:47:50,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:50,813] [INFO] Task started: CheckM
[2024-01-25 18:47:50,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000466945.1_ASM46694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000466945.1_ASM46694v1_genomic.fna/checkm_input GCF_000466945.1_ASM46694v1_genomic.fna/checkm_result
[2024-01-25 18:48:29,285] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:29,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:29,303] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:29,304] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:29,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000466945.1_ASM46694v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:29,305] [INFO] Task started: Blastn
[2024-01-25 18:48:29,305] [INFO] Running command: blastn -query GCF_000466945.1_ASM46694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d845f23-b939-49fb-b58f-41c51cd82ff2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000466945.1_ASM46694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:30,800] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:30,803] [INFO] Selected 26 target genomes.
[2024-01-25 18:48:30,803] [INFO] Target genome list was writen to GCF_000466945.1_ASM46694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:30,825] [INFO] Task started: fastANI
[2024-01-25 18:48:30,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b962423-7300-430b-aeb0-f3ceda91a763/GCF_000466945.1_ASM46694v1_genomic.fna.gz --refList GCF_000466945.1_ASM46694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000466945.1_ASM46694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:49,389] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:49,404] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:49,405] [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_003860345.1	s__Caenibius tardaugens	99.9981	1406	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001305965.1	s__Caenibius sp001305965	78.7226	340	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625325.1	s__Caenibius estronivorus	78.6981	427	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	78.2987	351	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652615.1	s__Novosphingobium arvoryzae	78.2555	322	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	78.0773	285	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694345.1	s__Novosphingobium jiangmenense	78.0387	278	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.9947	314	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_007830315.1	s__Novosphingobium taihuense	77.9411	247	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002198665.1	s__Novosphingobium sp002198665	77.9304	284	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.9278	307	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827515.1	s__Pelagerythrobacter marinus	77.8943	256	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	77.8942	253	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001650725.1	s__Sphingobium sp001650725	77.8638	220	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCA_017744735.1	s__Caenibius sp017744735	77.8587	282	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_003605755.1	s__Tsuneonella suprasediminis	77.8357	251	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	77.8098	237	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	77.7726	194	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807925.1	s__Novosphingobium subterraneum	77.7594	280	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.63	97.57	0.88	0.77	4	-
GCF_001014975.1	s__Novosphingobium sp002336885	77.7421	336	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_001634625.1	s__Croceicoccus bisphenolivorans	77.7077	247	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	77.6917	223	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_014230315.1	s__Novosphingobium flavum	77.6818	271	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832325.1	s__Novosphingobium sp903832325	77.5153	276	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.98	99.94	0.97	0.96	4	-
GCF_016745095.1	s__Croceicoccus sp016745095	77.3732	221	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	77.0475	185	1406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:49,406] [INFO] GTDB search result was written to GCF_000466945.1_ASM46694v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:49,407] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:49,411] [INFO] DFAST_QC result json was written to GCF_000466945.1_ASM46694v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:49,411] [INFO] DFAST_QC completed!
[2024-01-25 18:48:49,411] [INFO] Total running time: 0h1m29s