[2024-01-24 13:56:12,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference
[2024-01-24 13:56:14,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,423] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f92a77d-357f-4b9b-93f4-0761fe1cc868/GCF_000423485.1_ASM42348v1_genomic.fna.gz | prodigal -d GCF_000423485.1_ASM42348v1_genomic.fna/cds.fna -a GCF_000423485.1_ASM42348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:19,825] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:19,825] [INFO] Task started: HMMsearch
[2024-01-24 13:56:19,825] [INFO] Running command: hmmsearch --tblout GCF_000423485.1_ASM42348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference/reference_markers.hmm GCF_000423485.1_ASM42348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:20,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:20,089] [INFO] Found 6/6 markers.
[2024-01-24 13:56:20,113] [INFO] Query marker FASTA was written to GCF_000423485.1_ASM42348v1_genomic.fna/markers.fasta
[2024-01-24 13:56:20,114] [INFO] Task started: Blastn
[2024-01-24 13:56:20,114] [INFO] Running command: blastn -query GCF_000423485.1_ASM42348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference/reference_markers.fasta -out GCF_000423485.1_ASM42348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:21,009] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:21,014] [INFO] Selected 25 target genomes.
[2024-01-24 13:56:21,015] [INFO] Target genome list was writen to GCF_000423485.1_ASM42348v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:21,026] [INFO] Task started: fastANI
[2024-01-24 13:56:21,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f92a77d-357f-4b9b-93f4-0761fe1cc868/GCF_000423485.1_ASM42348v1_genomic.fna.gz --refList GCF_000423485.1_ASM42348v1_genomic.fna/target_genomes.txt --output GCF_000423485.1_ASM42348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:37,683] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:37,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:37,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:37,696] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:37,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:37,697] [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
Propionimicrobium lymphophilum	strain=DSM 4903	GCA_000423485.1	33012	33012	type	True	100.0	666	666	95	conclusive
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	77.5635	58	666	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	77.2865	63	666	95	below_threshold
Brooklawnia cerclae	strain=DSM 19609	GCA_011758645.1	349934	349934	type	True	77.2835	82	666	95	below_threshold
Propionibacterium australiense	strain=NCTC13651	GCA_900637915.1	119981	119981	type	True	77.1496	82	666	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	77.1074	64	666	95	below_threshold
Luteococcus japonicus	strain=DSM 10546	GCA_003752415.1	33984	33984	type	True	77.0941	61	666	95	below_threshold
Propionibacterium acidifaciens	strain=DSM 21887	GCA_000426605.1	556499	556499	type	True	77.0629	79	666	95	below_threshold
Propionibacterium freudenreichii subsp. freudenreichii	strain=DSM 20271	GCA_000940845.1	66712	1744	type	True	76.9754	81	666	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	76.9366	63	666	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	76.7915	79	666	95	below_threshold
Aestuariimicrobium kwangyangense	strain=DSM 21549	GCA_000421525.1	396389	396389	type	True	76.7436	55	666	95	below_threshold
Propionibacterium cyclohexanicum	strain=DSM 16859	GCA_900111365.1	64702	64702	type	True	76.5428	52	666	95	below_threshold
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	76.4332	55	666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,699] [INFO] DFAST Taxonomy check result was written to GCF_000423485.1_ASM42348v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:37,699] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:37,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:37,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference/checkm_data
[2024-01-24 13:56:37,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:37,732] [INFO] Task started: CheckM
[2024-01-24 13:56:37,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423485.1_ASM42348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423485.1_ASM42348v1_genomic.fna/checkm_input GCF_000423485.1_ASM42348v1_genomic.fna/checkm_result
[2024-01-24 13:57:00,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:00,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:00,550] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:00,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:00,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423485.1_ASM42348v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:00,551] [INFO] Task started: Blastn
[2024-01-24 13:57:00,552] [INFO] Running command: blastn -query GCF_000423485.1_ASM42348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b32a72f-4878-484d-a06b-a2751e72db60/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423485.1_ASM42348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:01,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:01,828] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:01,828] [INFO] Target genome list was writen to GCF_000423485.1_ASM42348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:01,850] [INFO] Task started: fastANI
[2024-01-24 13:57:01,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f92a77d-357f-4b9b-93f4-0761fe1cc868/GCF_000423485.1_ASM42348v1_genomic.fna.gz --refList GCF_000423485.1_ASM42348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423485.1_ASM42348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:14,770] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:14,816] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:14,816] [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_000423485.1	s__Propionimicrobium lymphophilum	100.0	665	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionimicrobium	95.0	97.98	97.94	0.90	0.89	3	conclusive
GCF_001997345.1	s__Arachnia aquimaris	77.2865	63	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758645.1	s__Brooklawnia cerclae	77.2835	82	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brooklawnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000940845.1	s__Propionibacterium freudenreichii	77.196	81	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	98.89	98.71	0.93	0.90	43	-
GCF_001998865.1	s__Arachnia flavescens	77.1074	64	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426605.1	s__Propionibacterium acidifaciens	77.0629	79	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.24	99.02	0.93	0.90	4	-
GCA_011174705.1	s__Arachnia coleopterorum	76.9366	63	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666605.1	s__Propionibacterium australiense	76.7915	79	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.91	99.75	0.98	0.97	4	-
GCF_000421525.1	s__Aestuariimicrobium kwangyangense	76.7436	55	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693815.1	s__Arachnia lapidicapta	76.6762	56	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.86	97.76	0.95	0.93	4	-
GCF_900111365.1	s__Propionibacterium cyclohexanicum	76.5428	52	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900289195.1	s__Propionibacterium sp900289195	76.5407	83	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.03	99.03	0.94	0.94	2	-
GCF_900092135.1	s__Raineyella antarctica	76.4332	55	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002843035.1	s__Propionicimonas sp002843035	76.333	52	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	76.2399	52	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:14,818] [INFO] GTDB search result was written to GCF_000423485.1_ASM42348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:14,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:14,826] [INFO] DFAST_QC result json was written to GCF_000423485.1_ASM42348v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:14,826] [INFO] DFAST_QC completed!
[2024-01-24 13:57:14,826] [INFO] Total running time: 0h1m2s