[2024-01-24 14:31:14,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference
[2024-01-24 14:31:16,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,096] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,097] [INFO] Running command: gunzip -c /var/lib/cwl/stg26c488f7-0833-410a-a16a-0aa73110dfa2/GCF_005818865.1_ASM581886v1_genomic.fna.gz | prodigal -d GCF_005818865.1_ASM581886v1_genomic.fna/cds.fna -a GCF_005818865.1_ASM581886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:25,307] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:25,308] [INFO] Task started: HMMsearch
[2024-01-24 14:31:25,308] [INFO] Running command: hmmsearch --tblout GCF_005818865.1_ASM581886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference/reference_markers.hmm GCF_005818865.1_ASM581886v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:25,566] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:25,567] [INFO] Found 6/6 markers.
[2024-01-24 14:31:25,599] [INFO] Query marker FASTA was written to GCF_005818865.1_ASM581886v1_genomic.fna/markers.fasta
[2024-01-24 14:31:25,600] [INFO] Task started: Blastn
[2024-01-24 14:31:25,600] [INFO] Running command: blastn -query GCF_005818865.1_ASM581886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference/reference_markers.fasta -out GCF_005818865.1_ASM581886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:26,222] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:26,226] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:26,226] [INFO] Target genome list was writen to GCF_005818865.1_ASM581886v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:26,239] [INFO] Task started: fastANI
[2024-01-24 14:31:26,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c488f7-0833-410a-a16a-0aa73110dfa2/GCF_005818865.1_ASM581886v1_genomic.fna.gz --refList GCF_005818865.1_ASM581886v1_genomic.fna/target_genomes.txt --output GCF_005818865.1_ASM581886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:43,468] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:43,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:43,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:43,476] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:43,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:43,476] [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
Mariprofundus erugo	strain=P3	GCA_005818865.1	2528639	2528639	type	True	100.0	948	950	95	conclusive
Mariprofundus ferrooxydans	strain=PV-1	GCA_000153765.1	314344	314344	suspected-type	True	77.9168	262	950	95	below_threshold
Mariprofundus ferrinatatus	strain=CP-8	GCA_002795825.1	1921087	1921087	type	True	77.2123	140	950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:43,479] [INFO] DFAST Taxonomy check result was written to GCF_005818865.1_ASM581886v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:43,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:43,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:43,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference/checkm_data
[2024-01-24 14:31:43,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:43,515] [INFO] Task started: CheckM
[2024-01-24 14:31:43,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005818865.1_ASM581886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005818865.1_ASM581886v1_genomic.fna/checkm_input GCF_005818865.1_ASM581886v1_genomic.fna/checkm_result
[2024-01-24 14:32:15,791] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:15,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:15,814] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:15,814] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:15,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005818865.1_ASM581886v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:15,815] [INFO] Task started: Blastn
[2024-01-24 14:32:15,815] [INFO] Running command: blastn -query GCF_005818865.1_ASM581886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb3ac2ef-08b9-4c88-a662-bfd93e3ec193/dqc_reference/reference_markers_gtdb.fasta -out GCF_005818865.1_ASM581886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:16,617] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:16,621] [INFO] Selected 18 target genomes.
[2024-01-24 14:32:16,621] [INFO] Target genome list was writen to GCF_005818865.1_ASM581886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:16,649] [INFO] Task started: fastANI
[2024-01-24 14:32:16,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c488f7-0833-410a-a16a-0aa73110dfa2/GCF_005818865.1_ASM581886v1_genomic.fna.gz --refList GCF_005818865.1_ASM581886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005818865.1_ASM581886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:26,453] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:26,469] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:26,470] [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_005818865.1	s__Mariprofundus erugo	100.0	948	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	98.87	98.87	0.91	0.91	2	conclusive
GCF_000153765.1	s__Mariprofundus ferrooxydans	77.9168	262	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	98.65	97.77	0.90	0.87	4	-
GCA_002791575.1	s__Mariprofundus sp002791575	77.6357	297	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	99.85	99.62	0.94	0.91	4	-
GCF_002795825.1	s__Mariprofundus ferrinatatus	77.2123	140	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387475.1	s__Mariprofundus sp013387475	77.1548	171	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387455.1	s__Mariprofundus sp013387455	76.8813	168	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001895085.1	s__Mariprofundus micogutta	76.5876	129	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003665155.1	s__Mariprofundus sp003665155	76.5862	89	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485035.1	s__Mariprofundus sp015485035	76.5839	118	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__Mariprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002791545.1	s__CG1-02-49-23 sp002791545	76.5616	70	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__CG1-02-49-23	95.0	99.93	99.78	0.91	0.84	6	-
GCA_001871195.1	s__UBA1543 sp001871195	76.2942	93	950	d__Bacteria;p__Proteobacteria;c__Zetaproteobacteria;o__Mariprofundales;f__Mariprofundaceae;g__UBA1543	95.0	99.98	99.95	0.97	0.97	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:26,471] [INFO] GTDB search result was written to GCF_005818865.1_ASM581886v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:26,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:26,475] [INFO] DFAST_QC result json was written to GCF_005818865.1_ASM581886v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:26,475] [INFO] DFAST_QC completed!
[2024-01-24 14:32:26,475] [INFO] Total running time: 0h1m12s