[2024-01-24 13:57:43,728] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference
[2024-01-24 13:57:44,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,978] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg85829a22-ed4c-4696-88bb-6710669288a5/GCF_002080475.1_ASM208047v1_genomic.fna.gz | prodigal -d GCF_002080475.1_ASM208047v1_genomic.fna/cds.fna -a GCF_002080475.1_ASM208047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:53,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:53,775] [INFO] Task started: HMMsearch
[2024-01-24 13:57:53,775] [INFO] Running command: hmmsearch --tblout GCF_002080475.1_ASM208047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference/reference_markers.hmm GCF_002080475.1_ASM208047v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:54,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:54,091] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg85829a22-ed4c-4696-88bb-6710669288a5/GCF_002080475.1_ASM208047v1_genomic.fna.gz]
[2024-01-24 13:57:54,141] [INFO] Query marker FASTA was written to GCF_002080475.1_ASM208047v1_genomic.fna/markers.fasta
[2024-01-24 13:57:54,141] [INFO] Task started: Blastn
[2024-01-24 13:57:54,141] [INFO] Running command: blastn -query GCF_002080475.1_ASM208047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference/reference_markers.fasta -out GCF_002080475.1_ASM208047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:54,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:54,749] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:54,749] [INFO] Target genome list was writen to GCF_002080475.1_ASM208047v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:54,843] [INFO] Task started: fastANI
[2024-01-24 13:57:54,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg85829a22-ed4c-4696-88bb-6710669288a5/GCF_002080475.1_ASM208047v1_genomic.fna.gz --refList GCF_002080475.1_ASM208047v1_genomic.fna/target_genomes.txt --output GCF_002080475.1_ASM208047v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:03,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:03,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:03,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:03,010] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:03,010] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:03,011] [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
Clostridium formicaceticum	strain=DSM 92	GCA_002080475.1	1497	1497	type	True	100.0	1528	1528	95	conclusive
Clostridium formicaceticum	strain=ATCC 27076	GCA_001854185.1	1497	1497	type	True	99.9972	1528	1528	95	conclusive
Clostridium aceticum	strain=DSM 1496	GCA_001042715.1	84022	84022	type	True	83.9499	914	1528	95	below_threshold
Clostridium aceticum	strain=DSM 1496	GCA_000949285.1	84022	84022	type	True	83.7769	893	1528	95	below_threshold
Anaerovirgula multivorans	strain=SCA	GCA_900188145.1	312168	312168	type	True	78.7162	436	1528	95	below_threshold
Natronincola ferrireducens	strain=DSM 18346	GCA_900100845.1	393762	393762	type	True	78.1121	288	1528	95	below_threshold
Natronincola peptidivorans	strain=DSM 18979	GCA_900111615.1	426128	426128	type	True	77.7554	271	1528	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,013] [INFO] DFAST Taxonomy check result was written to GCF_002080475.1_ASM208047v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:03,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:03,013] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:03,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference/checkm_data
[2024-01-24 13:58:03,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:03,065] [INFO] Task started: CheckM
[2024-01-24 13:58:03,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002080475.1_ASM208047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002080475.1_ASM208047v1_genomic.fna/checkm_input GCF_002080475.1_ASM208047v1_genomic.fna/checkm_result
[2024-01-24 13:58:36,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:36,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,331] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:36,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:36,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002080475.1_ASM208047v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:36,332] [INFO] Task started: Blastn
[2024-01-24 13:58:36,332] [INFO] Running command: blastn -query GCF_002080475.1_ASM208047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab7e4e6a-7c11-4510-9741-3760baafa3ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_002080475.1_ASM208047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,100] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,103] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:37,103] [INFO] Target genome list was writen to GCF_002080475.1_ASM208047v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:37,135] [INFO] Task started: fastANI
[2024-01-24 13:58:37,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg85829a22-ed4c-4696-88bb-6710669288a5/GCF_002080475.1_ASM208047v1_genomic.fna.gz --refList GCF_002080475.1_ASM208047v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002080475.1_ASM208047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:45,948] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:45,957] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:45,957] [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_001854185.1	s__Clostridium_W formicaceticum	99.9972	1528	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Clostridium_W	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001042715.1	s__Clostridium_W aceticum	83.9699	913	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Clostridium_W	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000016985.1	s__Alkaliphilus_A metalliredigens	79.4198	163	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188145.1	s__Anaerovirgula multivorans	78.6803	441	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Anaerovirgula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141165.1	s__Alkaliphilus_B sp018141165	78.3393	109	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100845.1	s__Natronincola ferrireducens	78.1246	287	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111615.1	s__Natronincola_A peptidivorans	77.7533	270	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521085.1	s__JAAYNB01 sp012521085	76.905	89	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__JAAYNB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621485.1	s__Alkaliphilus transvaalensis	76.6557	107	1528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:45,958] [INFO] GTDB search result was written to GCF_002080475.1_ASM208047v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:45,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:45,962] [INFO] DFAST_QC result json was written to GCF_002080475.1_ASM208047v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:45,962] [INFO] DFAST_QC completed!
[2024-01-24 13:58:45,962] [INFO] Total running time: 0h1m2s