[2024-01-24 13:28:01,775] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference
[2024-01-24 13:28:03,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,157] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,157] [INFO] Running command: gunzip -c /var/lib/cwl/stgab5c9338-512e-48cc-823a-a7353b0de146/GCF_007859945.1_ASM785994v1_genomic.fna.gz | prodigal -d GCF_007859945.1_ASM785994v1_genomic.fna/cds.fna -a GCF_007859945.1_ASM785994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:18,136] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:18,136] [INFO] Task started: HMMsearch
[2024-01-24 13:28:18,136] [INFO] Running command: hmmsearch --tblout GCF_007859945.1_ASM785994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference/reference_markers.hmm GCF_007859945.1_ASM785994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:18,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:18,395] [INFO] Found 6/6 markers.
[2024-01-24 13:28:18,434] [INFO] Query marker FASTA was written to GCF_007859945.1_ASM785994v1_genomic.fna/markers.fasta
[2024-01-24 13:28:18,435] [INFO] Task started: Blastn
[2024-01-24 13:28:18,435] [INFO] Running command: blastn -query GCF_007859945.1_ASM785994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference/reference_markers.fasta -out GCF_007859945.1_ASM785994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:19,085] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:19,089] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:19,090] [INFO] Target genome list was writen to GCF_007859945.1_ASM785994v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:19,094] [INFO] Task started: fastANI
[2024-01-24 13:28:19,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgab5c9338-512e-48cc-823a-a7353b0de146/GCF_007859945.1_ASM785994v1_genomic.fna.gz --refList GCF_007859945.1_ASM785994v1_genomic.fna/target_genomes.txt --output GCF_007859945.1_ASM785994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:33,708] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:33,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:33,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:33,718] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:33,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:33,719] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	100.0	1685	1686	95	conclusive
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	78.7543	548	1686	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	78.6472	602	1686	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	78.6016	604	1686	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	78.2776	540	1686	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	78.1958	315	1686	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	77.9755	506	1686	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	76.7658	198	1686	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	74.8327	141	1686	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:33,721] [INFO] DFAST Taxonomy check result was written to GCF_007859945.1_ASM785994v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:33,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:33,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:33,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference/checkm_data
[2024-01-24 13:28:33,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:33,771] [INFO] Task started: CheckM
[2024-01-24 13:28:33,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859945.1_ASM785994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859945.1_ASM785994v1_genomic.fna/checkm_input GCF_007859945.1_ASM785994v1_genomic.fna/checkm_result
[2024-01-24 13:29:16,107] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:16,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:16,124] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:16,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:16,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859945.1_ASM785994v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:16,125] [INFO] Task started: Blastn
[2024-01-24 13:29:16,125] [INFO] Running command: blastn -query GCF_007859945.1_ASM785994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf63c1a-fedd-4ec4-877d-a8c761a72067/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859945.1_ASM785994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:17,051] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:17,054] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:17,055] [INFO] Target genome list was writen to GCF_007859945.1_ASM785994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:17,061] [INFO] Task started: fastANI
[2024-01-24 13:29:17,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgab5c9338-512e-48cc-823a-a7353b0de146/GCF_007859945.1_ASM785994v1_genomic.fna.gz --refList GCF_007859945.1_ASM785994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859945.1_ASM785994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:29,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:29,480] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:29,480] [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_007859945.1	s__Pseudobythopirellula maris	100.0	1685	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859955.1	s__Botrimarina colliarenosi	78.7655	546	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	78.7472	572	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	78.6182	605	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	78.5767	608	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753265.1	s__Botrimarina mediterranea	78.2647	543	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	99.49	99.49	0.94	0.94	2	-
GCF_007750855.1	s__Pirellulimonas nuda	77.9595	509	1686	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:29,482] [INFO] GTDB search result was written to GCF_007859945.1_ASM785994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:29,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:29,485] [INFO] DFAST_QC result json was written to GCF_007859945.1_ASM785994v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:29,485] [INFO] DFAST_QC completed!
[2024-01-24 13:29:29,485] [INFO] Total running time: 0h1m28s