[2024-01-24 13:40:42,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,862] [INFO] DQC Reference Directory: /var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference
[2024-01-24 13:40:44,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,213] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg6906a8a3-b098-4847-8ca5-161c04326238/GCF_000420425.1_ASM42042v1_genomic.fna.gz | prodigal -d GCF_000420425.1_ASM42042v1_genomic.fna/cds.fna -a GCF_000420425.1_ASM42042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,267] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,267] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,267] [INFO] Running command: hmmsearch --tblout GCF_000420425.1_ASM42042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference/reference_markers.hmm GCF_000420425.1_ASM42042v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:52,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:52,552] [INFO] Found 6/6 markers.
[2024-01-24 13:40:52,574] [INFO] Query marker FASTA was written to GCF_000420425.1_ASM42042v1_genomic.fna/markers.fasta
[2024-01-24 13:40:52,575] [INFO] Task started: Blastn
[2024-01-24 13:40:52,575] [INFO] Running command: blastn -query GCF_000420425.1_ASM42042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference/reference_markers.fasta -out GCF_000420425.1_ASM42042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:53,353] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:53,357] [INFO] Selected 21 target genomes.
[2024-01-24 13:40:53,358] [INFO] Target genome list was writen to GCF_000420425.1_ASM42042v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:53,381] [INFO] Task started: fastANI
[2024-01-24 13:40:53,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg6906a8a3-b098-4847-8ca5-161c04326238/GCF_000420425.1_ASM42042v1_genomic.fna.gz --refList GCF_000420425.1_ASM42042v1_genomic.fna/target_genomes.txt --output GCF_000420425.1_ASM42042v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:03,706] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:03,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:03,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:03,718] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:03,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:03,718] [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
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	100.0	771	773	95	conclusive
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	78.6556	147	773	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	78.4583	113	773	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	78.4407	111	773	95	below_threshold
Schaalia suimastitidis	strain=DSM 15538	GCA_000429105.1	121163	121163	type	True	77.5271	78	773	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	77.4864	68	773	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	77.2506	69	773	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	77.1685	72	773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:03,721] [INFO] DFAST Taxonomy check result was written to GCF_000420425.1_ASM42042v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:03,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:03,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:03,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference/checkm_data
[2024-01-24 13:41:03,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:03,756] [INFO] Task started: CheckM
[2024-01-24 13:41:03,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420425.1_ASM42042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420425.1_ASM42042v1_genomic.fna/checkm_input GCF_000420425.1_ASM42042v1_genomic.fna/checkm_result
[2024-01-24 13:41:33,639] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:33,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,654] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:33,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:33,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420425.1_ASM42042v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:33,655] [INFO] Task started: Blastn
[2024-01-24 13:41:33,656] [INFO] Running command: blastn -query GCF_000420425.1_ASM42042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb973dce1-84f7-459e-80de-a9ac858b26e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420425.1_ASM42042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:34,647] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:34,651] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:34,651] [INFO] Target genome list was writen to GCF_000420425.1_ASM42042v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:34,688] [INFO] Task started: fastANI
[2024-01-24 13:41:34,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg6906a8a3-b098-4847-8ca5-161c04326238/GCF_000420425.1_ASM42042v1_genomic.fna.gz --refList GCF_000420425.1_ASM42042v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420425.1_ASM42042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:44,897] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:44,911] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:44,911] [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_000420425.1	s__Pauljensenia vaccimaxillae	100.0	771	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005696695.1	s__Pauljensenia odontolytica_C	78.9187	134	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCA_001072465.1	s__Pauljensenia sp001072465	78.8916	130	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_000278725.1	s__Pauljensenia sp000278725	78.874	126	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.30	95.28	0.90	0.88	4	-
GCA_902373545.1	s__Pauljensenia sp902373545	78.8293	102	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.43	97.43	0.84	0.84	2	-
GCF_009730335.1	s__Pauljensenia odontolytica_A	78.74	146	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.93	96.74	0.95	0.91	4	-
GCF_001838165.1	s__Pauljensenia sp001838165	78.7003	141	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCF_014208035.1	s__Pauljensenia hyovaginalis	78.6561	146	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
GCA_018375675.1	s__Pauljensenia sp018375675	78.5704	139	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411415.1	s__Pauljensenia sp000411415	78.5453	150	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCF_900105015.1	s__Pauljensenia meyeri	78.4759	110	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	99.29	98.87	0.96	0.95	4	-
GCF_018986735.1	s__Pauljensenia sp018986735	78.459	131	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038885.2	s__Pauljensenia sp011038875	78.423	120	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.18	98.18	0.90	0.90	2	-
GCF_000758755.1	s__Pauljensenia sp000758755	78.189	86	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.30	97.11	0.96	0.96	3	-
GCF_900155595.1	s__Pauljensenia mediterranea	77.8555	159	773	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,913] [INFO] GTDB search result was written to GCF_000420425.1_ASM42042v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:44,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:44,917] [INFO] DFAST_QC result json was written to GCF_000420425.1_ASM42042v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:44,918] [INFO] DFAST_QC completed!
[2024-01-24 13:41:44,918] [INFO] Total running time: 0h1m2s