[2024-01-24 12:31:34,024] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference
[2024-01-24 12:31:35,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,256] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg47e6bc6e-43a5-418c-8705-eb6744b2ea5f/GCF_009184905.1_ASM918490v1_genomic.fna.gz | prodigal -d GCF_009184905.1_ASM918490v1_genomic.fna/cds.fna -a GCF_009184905.1_ASM918490v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:46,016] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:46,016] [INFO] Task started: HMMsearch
[2024-01-24 12:31:46,017] [INFO] Running command: hmmsearch --tblout GCF_009184905.1_ASM918490v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference/reference_markers.hmm GCF_009184905.1_ASM918490v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:46,267] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:46,269] [INFO] Found 6/6 markers.
[2024-01-24 12:31:46,304] [INFO] Query marker FASTA was written to GCF_009184905.1_ASM918490v1_genomic.fna/markers.fasta
[2024-01-24 12:31:46,304] [INFO] Task started: Blastn
[2024-01-24 12:31:46,304] [INFO] Running command: blastn -query GCF_009184905.1_ASM918490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference/reference_markers.fasta -out GCF_009184905.1_ASM918490v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:47,284] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:47,289] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:47,290] [INFO] Target genome list was writen to GCF_009184905.1_ASM918490v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:47,301] [INFO] Task started: fastANI
[2024-01-24 12:31:47,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e6bc6e-43a5-418c-8705-eb6744b2ea5f/GCF_009184905.1_ASM918490v1_genomic.fna.gz --refList GCF_009184905.1_ASM918490v1_genomic.fna/target_genomes.txt --output GCF_009184905.1_ASM918490v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:04,814] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:04,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:04,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:04,835] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:04,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:04,835] [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
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	100.0	1210	1211	95	conclusive
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	80.051	507	1211	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.1412	506	1211	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	78.2788	290	1211	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.5563	211	1211	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	77.3831	191	1211	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.3498	171	1211	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.335	185	1211	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.2562	206	1211	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	77.127	191	1211	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.0138	136	1211	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	76.9502	111	1211	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.9409	188	1211	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.9279	166	1211	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	76.7627	174	1211	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.7495	174	1211	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.4562	160	1211	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.4353	119	1211	95	below_threshold
Methylobacterium bullatum	strain=LMG 24788	GCA_014845095.1	570505	570505	type	True	76.432	127	1211	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.4138	126	1211	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.4096	117	1211	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	76.3914	134	1211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:04,837] [INFO] DFAST Taxonomy check result was written to GCF_009184905.1_ASM918490v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:04,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:04,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:04,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference/checkm_data
[2024-01-24 12:32:04,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:04,877] [INFO] Task started: CheckM
[2024-01-24 12:32:04,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009184905.1_ASM918490v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009184905.1_ASM918490v1_genomic.fna/checkm_input GCF_009184905.1_ASM918490v1_genomic.fna/checkm_result
[2024-01-24 12:32:39,009] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:39,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:39,037] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:39,037] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:39,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009184905.1_ASM918490v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:39,038] [INFO] Task started: Blastn
[2024-01-24 12:32:39,038] [INFO] Running command: blastn -query GCF_009184905.1_ASM918490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a711fdd-769b-4506-9ca8-12669ed46b1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009184905.1_ASM918490v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:40,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:40,942] [INFO] Selected 14 target genomes.
[2024-01-24 12:32:40,942] [INFO] Target genome list was writen to GCF_009184905.1_ASM918490v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:40,975] [INFO] Task started: fastANI
[2024-01-24 12:32:40,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e6bc6e-43a5-418c-8705-eb6744b2ea5f/GCF_009184905.1_ASM918490v1_genomic.fna.gz --refList GCF_009184905.1_ASM918490v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009184905.1_ASM918490v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:50,791] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:50,808] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:50,808] [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_009184905.1	s__Parvibaculum sedimenti	100.0	1210	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903889655.1	s__Parvibaculum sp903889655	83.2633	778	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.81	99.81	0.91	0.91	2	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	80.073	505	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	79.6038	505	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	79.5673	442	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	79.5632	548	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_017642695.1	s__Parvibaculum sp017642695	79.205	489	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCF_011762095.1	s__Parvibaculum indicum	79.132	507	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684405.1	s__Parvibaculum sp002684405	78.9359	406	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823365.1	s__Parvibaculum sp013823365	78.85	390	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	78.7453	329	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	77.3501	171	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	77.2174	210	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	76.8784	156	1211	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:50,810] [INFO] GTDB search result was written to GCF_009184905.1_ASM918490v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:50,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:50,814] [INFO] DFAST_QC result json was written to GCF_009184905.1_ASM918490v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:50,814] [INFO] DFAST_QC completed!
[2024-01-24 12:32:50,815] [INFO] Total running time: 0h1m17s