[2024-01-24 12:31:34,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,191] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference
[2024-01-24 12:31:35,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,454] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,454] [INFO] Running command: gunzip -c /var/lib/cwl/stgde9fb741-ffe0-4bcf-bfca-721a246eb9c4/GCF_000294655.1_Pm_DSM120_genomic.fna.gz | prodigal -d GCF_000294655.1_Pm_DSM120_genomic.fna/cds.fna -a GCF_000294655.1_Pm_DSM120_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:46,620] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:46,621] [INFO] Task started: HMMsearch
[2024-01-24 12:31:46,621] [INFO] Running command: hmmsearch --tblout GCF_000294655.1_Pm_DSM120_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference/reference_markers.hmm GCF_000294655.1_Pm_DSM120_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:46,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:46,942] [INFO] Found 6/6 markers.
[2024-01-24 12:31:46,979] [INFO] Query marker FASTA was written to GCF_000294655.1_Pm_DSM120_genomic.fna/markers.fasta
[2024-01-24 12:31:46,979] [INFO] Task started: Blastn
[2024-01-24 12:31:46,979] [INFO] Running command: blastn -query GCF_000294655.1_Pm_DSM120_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference/reference_markers.fasta -out GCF_000294655.1_Pm_DSM120_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:47,711] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:47,716] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:47,717] [INFO] Target genome list was writen to GCF_000294655.1_Pm_DSM120_genomic.fna/target_genomes.txt
[2024-01-24 12:31:47,725] [INFO] Task started: fastANI
[2024-01-24 12:31:47,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgde9fb741-ffe0-4bcf-bfca-721a246eb9c4/GCF_000294655.1_Pm_DSM120_genomic.fna.gz --refList GCF_000294655.1_Pm_DSM120_genomic.fna/target_genomes.txt --output GCF_000294655.1_Pm_DSM120_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:00,023] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:00,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:00,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:00,036] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:00,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:00,036] [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
Magnetospirillum molischianum	strain=DSM 120	GCA_000294655.1	1083	1083	type	True	100.0	1239	1244	95	conclusive
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	78.6056	346	1244	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	78.3393	313	1244	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	78.3199	356	1244	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	78.3005	364	1244	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.6997	305	1244	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	77.6584	284	1244	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	77.5857	299	1244	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.4322	137	1244	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.2922	141	1244	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	75.884	64	1244	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.5686	106	1244	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	75.4567	62	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:00,038] [INFO] DFAST Taxonomy check result was written to GCF_000294655.1_Pm_DSM120_genomic.fna/tc_result.tsv
[2024-01-24 12:32:00,039] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:00,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:00,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference/checkm_data
[2024-01-24 12:32:00,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:00,087] [INFO] Task started: CheckM
[2024-01-24 12:32:00,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000294655.1_Pm_DSM120_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000294655.1_Pm_DSM120_genomic.fna/checkm_input GCF_000294655.1_Pm_DSM120_genomic.fna/checkm_result
[2024-01-24 12:32:35,691] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:35,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:35,713] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:35,713] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:35,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000294655.1_Pm_DSM120_genomic.fna/markers.fasta)
[2024-01-24 12:32:35,714] [INFO] Task started: Blastn
[2024-01-24 12:32:35,715] [INFO] Running command: blastn -query GCF_000294655.1_Pm_DSM120_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7836466-c9f0-4e9f-a934-132134c70623/dqc_reference/reference_markers_gtdb.fasta -out GCF_000294655.1_Pm_DSM120_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:36,796] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:36,800] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:36,800] [INFO] Target genome list was writen to GCF_000294655.1_Pm_DSM120_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:36,817] [INFO] Task started: fastANI
[2024-01-24 12:32:36,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgde9fb741-ffe0-4bcf-bfca-721a246eb9c4/GCF_000294655.1_Pm_DSM120_genomic.fna.gz --refList GCF_000294655.1_Pm_DSM120_genomic.fna/target_genomes_gtdb.txt --output GCF_000294655.1_Pm_DSM120_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:46,819] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:46,836] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:46,836] [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_000294655.1	s__Phaeospirillum molischianum	100.0	1239	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900108475.1	s__Phaeospirillum fulvum_A	85.8365	851	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442515.1	s__Phaeospirillum fulvum_B	85.8261	854	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901915.1	s__Phaeospirillum sp903901915	78.4924	360	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.99	99.99	0.95	0.95	2	-
GCF_902729425.1	s__Phaeospirillum sp902729425	78.4881	374	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	78.32	356	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	78.319	351	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	78.2966	353	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195125.1	s__Phaeospirillum sp016195125	78.2065	270	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853455.1	s__Phaeospirillum sp903853455	78.1939	388	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	77.5548	298	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCA_903941105.1	s__CAJANL01 sp903941105	77.4198	274	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869415.1	s__VGEI01 sp016869415	76.4252	51	1244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:46,838] [INFO] GTDB search result was written to GCF_000294655.1_Pm_DSM120_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:46,839] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:46,845] [INFO] DFAST_QC result json was written to GCF_000294655.1_Pm_DSM120_genomic.fna/dqc_result.json
[2024-01-24 12:32:46,845] [INFO] DFAST_QC completed!
[2024-01-24 12:32:46,845] [INFO] Total running time: 0h1m13s