[2024-01-25 17:46:05,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:05,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:05,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference
[2024-01-25 17:46:06,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:06,641] [INFO] Task started: Prodigal
[2024-01-25 17:46:06,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg30676494-4b54-402f-a2a0-18cb663521f0/GCF_030159835.1_ASM3015983v1_genomic.fna.gz | prodigal -d GCF_030159835.1_ASM3015983v1_genomic.fna/cds.fna -a GCF_030159835.1_ASM3015983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:16,219] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:16,220] [INFO] Task started: HMMsearch
[2024-01-25 17:46:16,220] [INFO] Running command: hmmsearch --tblout GCF_030159835.1_ASM3015983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference/reference_markers.hmm GCF_030159835.1_ASM3015983v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:16,461] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:16,462] [INFO] Found 6/6 markers.
[2024-01-25 17:46:16,495] [INFO] Query marker FASTA was written to GCF_030159835.1_ASM3015983v1_genomic.fna/markers.fasta
[2024-01-25 17:46:16,495] [INFO] Task started: Blastn
[2024-01-25 17:46:16,496] [INFO] Running command: blastn -query GCF_030159835.1_ASM3015983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference/reference_markers.fasta -out GCF_030159835.1_ASM3015983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:17,193] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:17,196] [INFO] Selected 21 target genomes.
[2024-01-25 17:46:17,196] [INFO] Target genome list was writen to GCF_030159835.1_ASM3015983v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:17,215] [INFO] Task started: fastANI
[2024-01-25 17:46:17,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg30676494-4b54-402f-a2a0-18cb663521f0/GCF_030159835.1_ASM3015983v1_genomic.fna.gz --refList GCF_030159835.1_ASM3015983v1_genomic.fna/target_genomes.txt --output GCF_030159835.1_ASM3015983v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:31,053] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:31,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:31,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:31,061] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:31,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:31,061] [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
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	99.9845	1168	1182	95	conclusive
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	77.0677	195	1182	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	76.9204	223	1182	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	76.9117	224	1182	95	below_threshold
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	76.7722	148	1182	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	76.7167	160	1182	95	below_threshold
Sneathiella aquimaris	strain=216LB-ZA1-12	GCA_012720095.1	2599305	2599305	type	True	76.6772	171	1182	95	below_threshold
Thalassospira marina	strain=CSC3H3	GCA_002844375.1	2048283	2048283	type	True	75.6125	70	1182	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.4838	57	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:31,062] [INFO] DFAST Taxonomy check result was written to GCF_030159835.1_ASM3015983v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:31,063] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:31,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:31,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference/checkm_data
[2024-01-25 17:46:31,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:31,099] [INFO] Task started: CheckM
[2024-01-25 17:46:31,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159835.1_ASM3015983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159835.1_ASM3015983v1_genomic.fna/checkm_input GCF_030159835.1_ASM3015983v1_genomic.fna/checkm_result
[2024-01-25 17:47:02,764] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:02,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:02,781] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:02,781] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:02,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159835.1_ASM3015983v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:02,782] [INFO] Task started: Blastn
[2024-01-25 17:47:02,782] [INFO] Running command: blastn -query GCF_030159835.1_ASM3015983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bfd3e8f-901c-4f19-af7f-e9c3065cdbfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159835.1_ASM3015983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:04,061] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:04,063] [INFO] Selected 21 target genomes.
[2024-01-25 17:47:04,064] [INFO] Target genome list was writen to GCF_030159835.1_ASM3015983v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:04,079] [INFO] Task started: fastANI
[2024-01-25 17:47:04,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg30676494-4b54-402f-a2a0-18cb663521f0/GCF_030159835.1_ASM3015983v1_genomic.fna.gz --refList GCF_030159835.1_ASM3015983v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159835.1_ASM3015983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:17,863] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:17,872] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:17,873] [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_012720115.1	s__Sneathiella chinensis	99.9845	1168	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428885.1	s__Sneathiella sp002428885	77.3056	240	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313765.1	s__Sneathiella sp017313765	77.081	194	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226265.1	s__Sneathiella sp006226265	76.9318	143	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694385.1	s__Sneathiella sp002694385	76.9265	239	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCF_009882935.1	s__Sneathiella chungangensis	76.9005	225	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002706985.1	s__Sneathiella sp002706985	76.8504	174	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
GCF_015143595.1	s__Sneathiella sp015143595	76.8329	160	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932565.1	s__Sneathiella limimaris	76.7722	148	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882915.1	s__Sneathiella litorea	76.7167	160	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720095.1	s__Sneathiella aquimaris	76.6768	170	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.9014	92	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796975.1	s__Ferrovibrio sp002796975	75.7068	50	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844375.1	s__Thalassospira marina	75.6125	70	1182	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.72	97.72	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:17,874] [INFO] GTDB search result was written to GCF_030159835.1_ASM3015983v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:17,875] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:17,877] [INFO] DFAST_QC result json was written to GCF_030159835.1_ASM3015983v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:17,877] [INFO] DFAST_QC completed!
[2024-01-25 17:47:17,877] [INFO] Total running time: 0h1m12s