[2024-01-24 11:35:34,591] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference
[2024-01-24 11:35:35,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,791] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg81390dce-3500-4f9d-ad9d-b82b95904519/GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna.gz | prodigal -d GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/cds.fna -a GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:41,486] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:41,487] [INFO] Task started: HMMsearch
[2024-01-24 11:35:41,487] [INFO] Running command: hmmsearch --tblout GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference/reference_markers.hmm GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:41,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:41,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg81390dce-3500-4f9d-ad9d-b82b95904519/GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna.gz]
[2024-01-24 11:35:41,768] [INFO] Query marker FASTA was written to GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/markers.fasta
[2024-01-24 11:35:41,769] [INFO] Task started: Blastn
[2024-01-24 11:35:41,769] [INFO] Running command: blastn -query GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference/reference_markers.fasta -out GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:42,411] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:42,414] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:42,415] [INFO] Target genome list was writen to GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:42,480] [INFO] Task started: fastANI
[2024-01-24 11:35:42,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg81390dce-3500-4f9d-ad9d-b82b95904519/GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna.gz --refList GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/target_genomes.txt --output GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:48,824] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:48,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:48,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:48,838] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:48,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:48,839] [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
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	100.0	1123	1124	95	conclusive
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	99.7304	1024	1124	95	conclusive
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_000154485.1	1547	1547	type	True	99.6757	1025	1124	95	conclusive
Erysipelatoclostridium ramosum	strain=FDAARGOS_906	GCA_016027135.1	1547	1547	type	True	99.6488	1028	1124	95	conclusive
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	81.116	455	1124	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	80.232	395	1124	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	80.1841	395	1124	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.6918	234	1124	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.6599	237	1124	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.6327	148	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:48,840] [INFO] DFAST Taxonomy check result was written to GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:48,840] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:48,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:48,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference/checkm_data
[2024-01-24 11:35:48,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:48,876] [INFO] Task started: CheckM
[2024-01-24 11:35:48,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/checkm_input GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/checkm_result
[2024-01-24 11:36:14,641] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:14,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,662] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:14,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:14,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/markers.fasta)
[2024-01-24 11:36:14,664] [INFO] Task started: Blastn
[2024-01-24 11:36:14,664] [INFO] Running command: blastn -query GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b53ccb7-5bf1-4327-9f0e-8e8fcd2b4b6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:15,502] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:15,506] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:15,506] [INFO] Target genome list was writen to GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:15,518] [INFO] Task started: fastANI
[2024-01-24 11:36:15,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg81390dce-3500-4f9d-ad9d-b82b95904519/GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna.gz --refList GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/target_genomes_gtdb.txt --output GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:22,144] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:22,156] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:22,157] [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_014131695.1	s__Erysipelatoclostridium ramosum	99.7304	1024	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.66	99.35	0.93	0.87	70	conclusive
GCF_900102365.1	s__Erysipelatoclostridium cocleatum	81.1298	439	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	-
GCF_000686665.1	s__Erysipelatoclostridium saccharogumia	80.4534	435	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018369555.1	s__Erysipelatoclostridium spiroforme_A	80.3703	356	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000508865.1	s__Erysipelatoclostridium sp000508865	80.3199	427	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	80.1976	394	1124	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	80.1037	426	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCF_003480255.1	s__Faecalibacillus sp003480255	78.7182	225	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCA_900538465.1	s__Longibaculum sp900538465	77.8828	181	1124	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:22,158] [INFO] GTDB search result was written to GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:22,159] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:22,162] [INFO] DFAST_QC result json was written to GCF_900660185.1_E_ramosum_CHUV1985.1_genomic.fna/dqc_result.json
[2024-01-24 11:36:22,162] [INFO] DFAST_QC completed!
[2024-01-24 11:36:22,162] [INFO] Total running time: 0h0m48s