[2024-01-24 12:46:35,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference
[2024-01-24 12:46:36,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,506] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dc606de-6bb6-473f-8cf3-511c173b1e46/GCF_003344965.1_ASM334496v1_genomic.fna.gz | prodigal -d GCF_003344965.1_ASM334496v1_genomic.fna/cds.fna -a GCF_003344965.1_ASM334496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:06,860] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:06,860] [INFO] Task started: HMMsearch
[2024-01-24 12:47:06,860] [INFO] Running command: hmmsearch --tblout GCF_003344965.1_ASM334496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference/reference_markers.hmm GCF_003344965.1_ASM334496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:07,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:07,182] [INFO] Found 6/6 markers.
[2024-01-24 12:47:07,244] [INFO] Query marker FASTA was written to GCF_003344965.1_ASM334496v1_genomic.fna/markers.fasta
[2024-01-24 12:47:07,244] [INFO] Task started: Blastn
[2024-01-24 12:47:07,244] [INFO] Running command: blastn -query GCF_003344965.1_ASM334496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference/reference_markers.fasta -out GCF_003344965.1_ASM334496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:08,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:08,483] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:08,483] [INFO] Target genome list was writen to GCF_003344965.1_ASM334496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:08,486] [INFO] Task started: fastANI
[2024-01-24 12:47:08,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc606de-6bb6-473f-8cf3-511c173b1e46/GCF_003344965.1_ASM334496v1_genomic.fna.gz --refList GCF_003344965.1_ASM334496v1_genomic.fna/target_genomes.txt --output GCF_003344965.1_ASM334496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:36,466] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:36,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:36,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:36,478] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:36,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:36,478] [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
Streptomyces paludis	strain=GSSD-12	GCA_003344965.1	2282738	2282738	type	True	100.0	2817	2818	95	conclusive
Streptomyces corynorhini	strain=AC230	GCA_003346515.1	2282652	2282652	type	True	87.4662	1674	2818	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	85.7272	1495	2818	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	85.6186	1624	2818	95	below_threshold
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	84.7883	1299	2818	95	below_threshold
Streptomyces odonnellii	strain=NRRL B-24891	GCA_000981895.1	1417980	1417980	type	True	84.5294	1372	2818	95	below_threshold
Streptomyces liangshanensis	strain=QMT-12	GCA_011694815.1	2717324	2717324	type	True	83.9069	1486	2818	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.5521	1343	2818	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	82.4833	1180	2818	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	82.3041	1331	2818	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	81.9541	1342	2818	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.5674	1002	2818	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	80.9333	1241	2818	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	80.7903	1390	2818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:36,480] [INFO] DFAST Taxonomy check result was written to GCF_003344965.1_ASM334496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:36,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:36,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:36,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference/checkm_data
[2024-01-24 12:47:36,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:36,555] [INFO] Task started: CheckM
[2024-01-24 12:47:36,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003344965.1_ASM334496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003344965.1_ASM334496v1_genomic.fna/checkm_input GCF_003344965.1_ASM334496v1_genomic.fna/checkm_result
[2024-01-24 12:49:40,136] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:40,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:40,162] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:40,163] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:40,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003344965.1_ASM334496v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:40,163] [INFO] Task started: Blastn
[2024-01-24 12:49:40,163] [INFO] Running command: blastn -query GCF_003344965.1_ASM334496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38e31042-69f3-4f08-aa12-317995fbaca9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003344965.1_ASM334496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:42,046] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:42,050] [INFO] Selected 11 target genomes.
[2024-01-24 12:49:42,050] [INFO] Target genome list was writen to GCF_003344965.1_ASM334496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:42,061] [INFO] Task started: fastANI
[2024-01-24 12:49:42,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc606de-6bb6-473f-8cf3-511c173b1e46/GCF_003344965.1_ASM334496v1_genomic.fna.gz --refList GCF_003344965.1_ASM334496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003344965.1_ASM334496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:04,828] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:04,838] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:04,838] [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_003344965.1	s__Streptomyces paludis	100.0	2817	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003346515.1	s__Streptomyces corynorhini	87.4778	1671	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718095.1	s__Streptomyces scopuliridis	85.559	1634	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_004151105.1	s__Streptomyces sp004151105	85.3603	1615	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700515.1	s__Streptomyces lushanensis	84.8095	1296	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981895.1	s__Streptomyces odonnellii	84.528	1372	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.86	95.86	0.85	0.85	2	-
GCF_011694815.1	s__Streptomyces liangshanensis	83.8395	1495	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010384365.1	s__Streptomyces sp010384365	82.9906	1444	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
GCF_900119365.1	s__Streptomyces atratus_B	82.2807	1349	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003846175.1	s__Streptomyces sp003846175	82.135	1436	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	81.9454	1344	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:50:04,840] [INFO] GTDB search result was written to GCF_003344965.1_ASM334496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:04,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:04,843] [INFO] DFAST_QC result json was written to GCF_003344965.1_ASM334496v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:04,843] [INFO] DFAST_QC completed!
[2024-01-24 12:50:04,843] [INFO] Total running time: 0h3m30s