[2024-01-24 14:22:14,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:14,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:14,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference
[2024-01-24 14:22:16,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:16,316] [INFO] Task started: Prodigal
[2024-01-24 14:22:16,317] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfd40dae-f261-4996-97b8-0b4dcbb20d0c/GCF_003024685.1_ASM302468v1_genomic.fna.gz | prodigal -d GCF_003024685.1_ASM302468v1_genomic.fna/cds.fna -a GCF_003024685.1_ASM302468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:21,072] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:21,072] [INFO] Task started: HMMsearch
[2024-01-24 14:22:21,072] [INFO] Running command: hmmsearch --tblout GCF_003024685.1_ASM302468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference/reference_markers.hmm GCF_003024685.1_ASM302468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:21,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:21,304] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbfd40dae-f261-4996-97b8-0b4dcbb20d0c/GCF_003024685.1_ASM302468v1_genomic.fna.gz]
[2024-01-24 14:22:21,334] [INFO] Query marker FASTA was written to GCF_003024685.1_ASM302468v1_genomic.fna/markers.fasta
[2024-01-24 14:22:21,335] [INFO] Task started: Blastn
[2024-01-24 14:22:21,335] [INFO] Running command: blastn -query GCF_003024685.1_ASM302468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference/reference_markers.fasta -out GCF_003024685.1_ASM302468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:21,923] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:21,927] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:21,928] [INFO] Target genome list was writen to GCF_003024685.1_ASM302468v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:21,932] [INFO] Task started: fastANI
[2024-01-24 14:22:21,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd40dae-f261-4996-97b8-0b4dcbb20d0c/GCF_003024685.1_ASM302468v1_genomic.fna.gz --refList GCF_003024685.1_ASM302468v1_genomic.fna/target_genomes.txt --output GCF_003024685.1_ASM302468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:29,877] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:29,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:29,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:29,888] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:29,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:29,888] [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	100.0	901	905	95	conclusive
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	89.5628	617	905	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.526	235	905	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	78.4665	242	905	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	78.462	168	905	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	78.4596	234	905	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	78.3828	240	905	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	78.2958	236	905	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	78.2735	231	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:29,890] [INFO] DFAST Taxonomy check result was written to GCF_003024685.1_ASM302468v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:29,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:29,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:29,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference/checkm_data
[2024-01-24 14:22:29,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:29,931] [INFO] Task started: CheckM
[2024-01-24 14:22:29,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024685.1_ASM302468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024685.1_ASM302468v1_genomic.fna/checkm_input GCF_003024685.1_ASM302468v1_genomic.fna/checkm_result
[2024-01-24 14:22:51,390] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:51,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,412] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:51,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:51,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024685.1_ASM302468v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:51,413] [INFO] Task started: Blastn
[2024-01-24 14:22:51,414] [INFO] Running command: blastn -query GCF_003024685.1_ASM302468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32492847-9576-49f5-9c85-5c8fccfe5a67/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024685.1_ASM302468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:52,303] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:52,306] [INFO] Selected 10 target genomes.
[2024-01-24 14:22:52,306] [INFO] Target genome list was writen to GCF_003024685.1_ASM302468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:52,310] [INFO] Task started: fastANI
[2024-01-24 14:22:52,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd40dae-f261-4996-97b8-0b4dcbb20d0c/GCF_003024685.1_ASM302468v1_genomic.fna.gz --refList GCF_003024685.1_ASM302468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024685.1_ASM302468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:57,094] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:57,101] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:57,102] [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	100.0	901	905	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	92.0364	467	905	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	89.6215	613	905	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	80.8785	379	905	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	79.5139	222	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	78.4639	259	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	78.4528	235	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCA_910588165.1	s__Fimiplasma sp910588165	76.9115	52	905	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Fimiplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:57,103] [INFO] GTDB search result was written to GCF_003024685.1_ASM302468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:57,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:57,106] [INFO] DFAST_QC result json was written to GCF_003024685.1_ASM302468v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:57,107] [INFO] DFAST_QC completed!
[2024-01-24 14:22:57,107] [INFO] Total running time: 0h0m42s