[2024-01-24 14:54:56,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference
[2024-01-24 14:54:58,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,001] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,002] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc5b2240-77e6-4d74-9e94-b3377ac9af9a/GCF_004337445.1_ASM433744v1_genomic.fna.gz | prodigal -d GCF_004337445.1_ASM433744v1_genomic.fna/cds.fna -a GCF_004337445.1_ASM433744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:07,411] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:07,412] [INFO] Task started: HMMsearch
[2024-01-24 14:55:07,412] [INFO] Running command: hmmsearch --tblout GCF_004337445.1_ASM433744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference/reference_markers.hmm GCF_004337445.1_ASM433744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:07,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:07,706] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbc5b2240-77e6-4d74-9e94-b3377ac9af9a/GCF_004337445.1_ASM433744v1_genomic.fna.gz]
[2024-01-24 14:55:07,735] [INFO] Query marker FASTA was written to GCF_004337445.1_ASM433744v1_genomic.fna/markers.fasta
[2024-01-24 14:55:07,735] [INFO] Task started: Blastn
[2024-01-24 14:55:07,735] [INFO] Running command: blastn -query GCF_004337445.1_ASM433744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference/reference_markers.fasta -out GCF_004337445.1_ASM433744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:08,771] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:08,774] [INFO] Selected 22 target genomes.
[2024-01-24 14:55:08,775] [INFO] Target genome list was writen to GCF_004337445.1_ASM433744v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:08,790] [INFO] Task started: fastANI
[2024-01-24 14:55:08,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc5b2240-77e6-4d74-9e94-b3377ac9af9a/GCF_004337445.1_ASM433744v1_genomic.fna.gz --refList GCF_004337445.1_ASM433744v1_genomic.fna/target_genomes.txt --output GCF_004337445.1_ASM433744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:24,747] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:24,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:24,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:24,765] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:24,765] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:24,765] [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
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	80.81	414	1048	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	80.7996	413	1048	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.3833	287	1048	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.3781	279	1048	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.2896	276	1048	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.2184	272	1048	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	78.0284	254	1048	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.9609	256	1048	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.8409	243	1048	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.5643	179	1048	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.5634	336	1048	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	77.3376	244	1048	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.3327	250	1048	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.2708	140	1048	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.1333	138	1048	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.9851	216	1048	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	76.8982	107	1048	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	76.8721	55	1048	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	76.5702	134	1048	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	76.1389	197	1048	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.1004	188	1048	95	below_threshold
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	75.4983	74	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:24,767] [INFO] DFAST Taxonomy check result was written to GCF_004337445.1_ASM433744v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:24,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:24,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:24,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference/checkm_data
[2024-01-24 14:55:24,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:24,805] [INFO] Task started: CheckM
[2024-01-24 14:55:24,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004337445.1_ASM433744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004337445.1_ASM433744v1_genomic.fna/checkm_input GCF_004337445.1_ASM433744v1_genomic.fna/checkm_result
[2024-01-24 14:55:56,769] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:56,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:56,792] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:56,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:56,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004337445.1_ASM433744v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:56,793] [INFO] Task started: Blastn
[2024-01-24 14:55:56,793] [INFO] Running command: blastn -query GCF_004337445.1_ASM433744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f5dddb-2ebe-4549-a95f-b85dd34de857/dqc_reference/reference_markers_gtdb.fasta -out GCF_004337445.1_ASM433744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:58,672] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:58,676] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:58,676] [INFO] Target genome list was writen to GCF_004337445.1_ASM433744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:58,692] [INFO] Task started: fastANI
[2024-01-24 14:55:58,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc5b2240-77e6-4d74-9e94-b3377ac9af9a/GCF_004337445.1_ASM433744v1_genomic.fna.gz --refList GCF_004337445.1_ASM433744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004337445.1_ASM433744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:08,165] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:08,183] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:08,183] [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_004337445.1	s__Parasulfuritortus cantonensis	100.0	1046	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013335435.1	s__Parasulfuritortus sp013335435	85.8892	595	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967275.1	s__Sulfuritortus calidifontis	80.8294	411	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016873935.1	s__PFJX01 sp016873935	80.4804	407	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002782005.1	s__Parasulfuritortus sp002782005	80.3624	357	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	99.86	99.81	0.92	0.91	9	-
GCA_009772925.1	s__PFJX01 sp009772925	80.3598	412	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.99	99.98	1.00	0.99	4	-
GCA_002360535.1	s__UBA3361 sp002360535	80.2714	420	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA3361	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219425.1	s__PFJX01 sp016219425	79.9841	378	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234655.1	s__Sulfuritortus sp016234655	79.9782	397	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703155.1	s__JADJCP01 sp016703155	79.9292	425	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__JADJCP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347615.1	s__UBA9220 sp002347615	78.4992	268	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA9220;g__UBA9220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208415.1	s__JACQYB01 sp016208415	77.8294	244	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324385.1	s__Gallionella kumadai	77.5632	179	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212015.1	s__28-57-27 sp006212015	77.2711	142	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__28-57-27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391275.1	s__FEB-7 sp011391275	76.3523	130	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:08,185] [INFO] GTDB search result was written to GCF_004337445.1_ASM433744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:08,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:08,191] [INFO] DFAST_QC result json was written to GCF_004337445.1_ASM433744v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:08,191] [INFO] DFAST_QC completed!
[2024-01-24 14:56:08,191] [INFO] Total running time: 0h1m12s