[2024-01-24 13:49:29,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference
[2024-01-24 13:49:30,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,903] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,903] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3a244e9-6c3d-4a3f-8746-36f87f32b68f/GCF_004342585.1_ASM434258v1_genomic.fna.gz | prodigal -d GCF_004342585.1_ASM434258v1_genomic.fna/cds.fna -a GCF_004342585.1_ASM434258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,216] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,217] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,217] [INFO] Running command: hmmsearch --tblout GCF_004342585.1_ASM434258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference/reference_markers.hmm GCF_004342585.1_ASM434258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:45,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:45,592] [INFO] Found 6/6 markers.
[2024-01-24 13:49:45,630] [INFO] Query marker FASTA was written to GCF_004342585.1_ASM434258v1_genomic.fna/markers.fasta
[2024-01-24 13:49:45,630] [INFO] Task started: Blastn
[2024-01-24 13:49:45,630] [INFO] Running command: blastn -query GCF_004342585.1_ASM434258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference/reference_markers.fasta -out GCF_004342585.1_ASM434258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,567] [INFO] Selected 25 target genomes.
[2024-01-24 13:49:46,567] [INFO] Target genome list was writen to GCF_004342585.1_ASM434258v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:46,577] [INFO] Task started: fastANI
[2024-01-24 13:49:46,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3a244e9-6c3d-4a3f-8746-36f87f32b68f/GCF_004342585.1_ASM434258v1_genomic.fna.gz --refList GCF_004342585.1_ASM434258v1_genomic.fna/target_genomes.txt --output GCF_004342585.1_ASM434258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:11,224] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:11,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:11,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:11,247] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:11,247] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:11,247] [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 aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.6153	427	1385	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	79.529	486	1385	95	below_threshold
Herbaspirillum chlorophenolicum	strain=CPW301	GCA_001189955.1	211589	211589	type	True	79.474	382	1385	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	79.3981	378	1385	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	79.3497	455	1385	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	79.3475	416	1385	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	79.3177	372	1385	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	79.2365	367	1385	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	79.2299	429	1385	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	79.1965	391	1385	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	79.1895	375	1385	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	79.0555	440	1385	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	79.0528	368	1385	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	79.0009	400	1385	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	78.9182	386	1385	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.8856	383	1385	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	78.8812	398	1385	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	78.8227	380	1385	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	78.7127	378	1385	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	78.6978	369	1385	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.6777	371	1385	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	78.4335	367	1385	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	78.3087	363	1385	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	78.2597	327	1385	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	78.1743	390	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:11,249] [INFO] DFAST Taxonomy check result was written to GCF_004342585.1_ASM434258v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:11,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:11,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:11,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference/checkm_data
[2024-01-24 13:50:11,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:11,294] [INFO] Task started: CheckM
[2024-01-24 13:50:11,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342585.1_ASM434258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342585.1_ASM434258v1_genomic.fna/checkm_input GCF_004342585.1_ASM434258v1_genomic.fna/checkm_result
[2024-01-24 13:50:55,391] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:55,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:55,414] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:55,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:55,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342585.1_ASM434258v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:55,416] [INFO] Task started: Blastn
[2024-01-24 13:50:55,416] [INFO] Running command: blastn -query GCF_004342585.1_ASM434258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0ed6ac0-2562-4528-83fe-4321d4f261d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342585.1_ASM434258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:57,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:57,123] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:57,123] [INFO] Target genome list was writen to GCF_004342585.1_ASM434258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:57,142] [INFO] Task started: fastANI
[2024-01-24 13:50:57,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3a244e9-6c3d-4a3f-8746-36f87f32b68f/GCF_004342585.1_ASM434258v1_genomic.fna.gz --refList GCF_004342585.1_ASM434258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342585.1_ASM434258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:10,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:10,316] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:10,316] [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_004342585.1	s__Paucimonas lemoignei	100.0	1383	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003537575.1	s__Paucimonas sp003537575	82.8417	761	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590835.1	s__Paucimonas sp003590835	82.1831	738	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114795.1	s__Paucimonas sp004114795	82.0122	707	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	79.7473	475	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	79.695	400	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	79.5299	485	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	79.3255	417	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	79.2943	391	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040945.1	s__Herbaspirillum seropedicae	79.2079	390	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	79.1462	376	1385	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	79.0408	442	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	78.8517	378	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_001584145.1	s__Collimonas fungivorans	78.8112	381	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:10,318] [INFO] GTDB search result was written to GCF_004342585.1_ASM434258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:10,319] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:10,324] [INFO] DFAST_QC result json was written to GCF_004342585.1_ASM434258v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:10,324] [INFO] DFAST_QC completed!
[2024-01-24 13:51:10,324] [INFO] Total running time: 0h1m41s