[2024-01-24 12:53:41,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference
[2024-01-24 12:53:42,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:42,763] [INFO] Task started: Prodigal
[2024-01-24 12:53:42,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dd806d2-853a-4f1c-8fbe-aab80209a811/GCF_001700515.1_ASM170051v1_genomic.fna.gz | prodigal -d GCF_001700515.1_ASM170051v1_genomic.fna/cds.fna -a GCF_001700515.1_ASM170051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:02,010] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:02,011] [INFO] Task started: HMMsearch
[2024-01-24 12:54:02,011] [INFO] Running command: hmmsearch --tblout GCF_001700515.1_ASM170051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference/reference_markers.hmm GCF_001700515.1_ASM170051v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:02,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:02,434] [INFO] Found 6/6 markers.
[2024-01-24 12:54:02,509] [INFO] Query marker FASTA was written to GCF_001700515.1_ASM170051v1_genomic.fna/markers.fasta
[2024-01-24 12:54:02,509] [INFO] Task started: Blastn
[2024-01-24 12:54:02,509] [INFO] Running command: blastn -query GCF_001700515.1_ASM170051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference/reference_markers.fasta -out GCF_001700515.1_ASM170051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:04,547] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:04,551] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:04,552] [INFO] Target genome list was writen to GCF_001700515.1_ASM170051v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:04,556] [INFO] Task started: fastANI
[2024-01-24 12:54:04,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd806d2-853a-4f1c-8fbe-aab80209a811/GCF_001700515.1_ASM170051v1_genomic.fna.gz --refList GCF_001700515.1_ASM170051v1_genomic.fna/target_genomes.txt --output GCF_001700515.1_ASM170051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:22,516] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:22,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:22,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:22,532] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:22,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:22,533] [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 lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	100.0	2164	2180	95	conclusive
Streptomyces odonnellii	strain=NRRL B-24891	GCA_000981895.1	1417980	1417980	type	True	88.4705	1535	2180	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	86.6919	1469	2180	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	86.5089	1406	2180	95	below_threshold
Streptomyces paludis	strain=GSSD-12	GCA_003344965.1	2282738	2282738	type	True	84.5373	1324	2180	95	below_threshold
Streptomyces corynorhini	strain=AC230	GCA_003346515.1	2282652	2282652	type	True	84.5232	1264	2180	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.5341	1183	2180	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	81.4684	1104	2180	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.4276	841	2180	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.3295	872	2180	95	below_threshold
Streptomyces fuscigenes	strain=JBL-20	GCA_021556455.1	1528880	1528880	type	True	81.292	863	2180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:22,534] [INFO] DFAST Taxonomy check result was written to GCF_001700515.1_ASM170051v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:22,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:22,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:22,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference/checkm_data
[2024-01-24 12:54:22,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:22,606] [INFO] Task started: CheckM
[2024-01-24 12:54:22,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001700515.1_ASM170051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001700515.1_ASM170051v1_genomic.fna/checkm_input GCF_001700515.1_ASM170051v1_genomic.fna/checkm_result
[2024-01-24 12:55:34,118] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:34,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:34,143] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:34,143] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:34,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001700515.1_ASM170051v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:34,144] [INFO] Task started: Blastn
[2024-01-24 12:55:34,145] [INFO] Running command: blastn -query GCF_001700515.1_ASM170051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f0f8397-c6ae-4136-8fe9-abb6e1707f0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001700515.1_ASM170051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:38,924] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:38,930] [INFO] Selected 8 target genomes.
[2024-01-24 12:55:38,930] [INFO] Target genome list was writen to GCF_001700515.1_ASM170051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:38,942] [INFO] Task started: fastANI
[2024-01-24 12:55:38,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dd806d2-853a-4f1c-8fbe-aab80209a811/GCF_001700515.1_ASM170051v1_genomic.fna.gz --refList GCF_001700515.1_ASM170051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001700515.1_ASM170051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:59,349] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:59,390] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:59,390] [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_001700515.1	s__Streptomyces lushanensis	100.0	2164	2180	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_000981895.1	s__Streptomyces odonnellii	88.4742	1535	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.86	95.86	0.85	0.85	2	-
GCF_000718095.1	s__Streptomyces scopuliridis	86.6854	1470	2180	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	86.3969	1537	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346515.1	s__Streptomyces corynorhini	84.5677	1259	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344965.1	s__Streptomyces paludis	84.5223	1325	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719775.1	s__Streptomyces sp000719775	84.1128	1293	2180	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	83.0342	1261	2180	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:59,394] [INFO] GTDB search result was written to GCF_001700515.1_ASM170051v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:59,398] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:59,410] [INFO] DFAST_QC result json was written to GCF_001700515.1_ASM170051v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:59,411] [INFO] DFAST_QC completed!
[2024-01-24 12:55:59,411] [INFO] Total running time: 0h2m18s