[2024-01-25 17:58:35,668] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,672] [INFO] DQC Reference Directory: /var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference
[2024-01-25 17:58:36,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,920] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ff74916-c5fc-42f6-942e-6115f5cabc6c/GCF_025566905.1_ASM2556690v1_genomic.fna.gz | prodigal -d GCF_025566905.1_ASM2556690v1_genomic.fna/cds.fna -a GCF_025566905.1_ASM2556690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:40,946] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:40,946] [INFO] Task started: HMMsearch
[2024-01-25 17:58:40,946] [INFO] Running command: hmmsearch --tblout GCF_025566905.1_ASM2556690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference/reference_markers.hmm GCF_025566905.1_ASM2556690v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:41,154] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:41,155] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8ff74916-c5fc-42f6-942e-6115f5cabc6c/GCF_025566905.1_ASM2556690v1_genomic.fna.gz]
[2024-01-25 17:58:41,179] [INFO] Query marker FASTA was written to GCF_025566905.1_ASM2556690v1_genomic.fna/markers.fasta
[2024-01-25 17:58:41,179] [INFO] Task started: Blastn
[2024-01-25 17:58:41,180] [INFO] Running command: blastn -query GCF_025566905.1_ASM2556690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference/reference_markers.fasta -out GCF_025566905.1_ASM2556690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:41,731] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:41,733] [INFO] Selected 16 target genomes.
[2024-01-25 17:58:41,734] [INFO] Target genome list was writen to GCF_025566905.1_ASM2556690v1_genomic.fna/target_genomes.txt
[2024-01-25 17:58:41,748] [INFO] Task started: fastANI
[2024-01-25 17:58:41,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff74916-c5fc-42f6-942e-6115f5cabc6c/GCF_025566905.1_ASM2556690v1_genomic.fna.gz --refList GCF_025566905.1_ASM2556690v1_genomic.fna/target_genomes.txt --output GCF_025566905.1_ASM2556690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:58:49,643] [INFO] Task succeeded: fastANI
[2024-01-25 17:58:49,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:58:49,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:58:49,651] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:58:49,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:58:49,651] [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
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	96.2119	731	893	95	conclusive
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	90.1515	626	893	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	78.5718	237	893	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	78.5015	157	893	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	78.4326	243	893	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	78.4054	227	893	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.3943	232	893	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	78.1696	238	893	95	below_threshold
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	78.1572	238	893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:58:49,653] [INFO] DFAST Taxonomy check result was written to GCF_025566905.1_ASM2556690v1_genomic.fna/tc_result.tsv
[2024-01-25 17:58:49,654] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:58:49,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:58:49,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference/checkm_data
[2024-01-25 17:58:49,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:58:49,683] [INFO] Task started: CheckM
[2024-01-25 17:58:49,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025566905.1_ASM2556690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025566905.1_ASM2556690v1_genomic.fna/checkm_input GCF_025566905.1_ASM2556690v1_genomic.fna/checkm_result
[2024-01-25 17:59:07,750] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:07,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:07,768] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:07,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:07,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025566905.1_ASM2556690v1_genomic.fna/markers.fasta)
[2024-01-25 17:59:07,769] [INFO] Task started: Blastn
[2024-01-25 17:59:07,769] [INFO] Running command: blastn -query GCF_025566905.1_ASM2556690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd176fceb-e321-4e0f-8899-67cce673a191/dqc_reference/reference_markers_gtdb.fasta -out GCF_025566905.1_ASM2556690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:08,526] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:08,528] [INFO] Selected 10 target genomes.
[2024-01-25 17:59:08,528] [INFO] Target genome list was writen to GCF_025566905.1_ASM2556690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:08,553] [INFO] Task started: fastANI
[2024-01-25 17:59:08,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff74916-c5fc-42f6-942e-6115f5cabc6c/GCF_025566905.1_ASM2556690v1_genomic.fna.gz --refList GCF_025566905.1_ASM2556690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025566905.1_ASM2556690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:13,794] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:13,800] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:59:13,801] [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_003024685.1	s__Faecalibacillus intestinalis	96.2119	731	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	conclusive
GCA_900544435.1	s__Faecalibacillus sp900544435	93.1729	464	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.05	98.83	0.79	0.74	3	-
GCF_003024675.1	s__Faecalibacillus faecis	90.1734	625	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.99	96.95	0.86	0.80	14	-
GCF_003480255.1	s__Faecalibacillus sp003480255	80.665	370	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCF_016901755.1	s__Faecalibacillus spiroforme_A	78.969	249	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	78.423	226	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	78.4007	256	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCA_017889095.1	s__Erysipelatoclostridium sp017889095	77.7225	206	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588165.1	s__Fimiplasma sp910588165	77.0986	50	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Fimiplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:13,802] [INFO] GTDB search result was written to GCF_025566905.1_ASM2556690v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:13,803] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:13,805] [INFO] DFAST_QC result json was written to GCF_025566905.1_ASM2556690v1_genomic.fna/dqc_result.json
[2024-01-25 17:59:13,805] [INFO] DFAST_QC completed!
[2024-01-25 17:59:13,805] [INFO] Total running time: 0h0m38s