[2024-01-24 13:45:48,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:48,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:48,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference
[2024-01-24 13:45:50,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:50,063] [INFO] Task started: Prodigal
[2024-01-24 13:45:50,063] [INFO] Running command: gunzip -c /var/lib/cwl/stg889636f1-eabb-4425-8689-b4455dce0fbd/GCF_008704555.1_ASM870455v1_genomic.fna.gz | prodigal -d GCF_008704555.1_ASM870455v1_genomic.fna/cds.fna -a GCF_008704555.1_ASM870455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:12,140] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:12,141] [INFO] Task started: HMMsearch
[2024-01-24 13:46:12,141] [INFO] Running command: hmmsearch --tblout GCF_008704555.1_ASM870455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference/reference_markers.hmm GCF_008704555.1_ASM870455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:12,573] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:12,574] [INFO] Found 6/6 markers.
[2024-01-24 13:46:12,655] [INFO] Query marker FASTA was written to GCF_008704555.1_ASM870455v1_genomic.fna/markers.fasta
[2024-01-24 13:46:12,656] [INFO] Task started: Blastn
[2024-01-24 13:46:12,656] [INFO] Running command: blastn -query GCF_008704555.1_ASM870455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference/reference_markers.fasta -out GCF_008704555.1_ASM870455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:13,997] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:14,001] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:14,001] [INFO] Target genome list was writen to GCF_008704555.1_ASM870455v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:14,014] [INFO] Task started: fastANI
[2024-01-24 13:46:14,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg889636f1-eabb-4425-8689-b4455dce0fbd/GCF_008704555.1_ASM870455v1_genomic.fna.gz --refList GCF_008704555.1_ASM870455v1_genomic.fna/target_genomes.txt --output GCF_008704555.1_ASM870455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:39,294] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:39,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:39,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:39,306] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:39,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:39,307] [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 nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	100.0	2527	2527	95	conclusive
Streptomyces nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	99.9768	2478	2527	95	conclusive
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	87.2742	1700	2527	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	86.1358	1701	2527	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	85.9555	1702	2527	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	85.8361	1662	2527	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.4541	1289	2527	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	84.2489	1497	2527	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	84.2136	1566	2527	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	84.1821	1437	2527	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.2626	1423	2527	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.0457	1272	2527	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.7634	1060	2527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:39,308] [INFO] DFAST Taxonomy check result was written to GCF_008704555.1_ASM870455v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:39,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:39,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:39,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference/checkm_data
[2024-01-24 13:46:39,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:39,386] [INFO] Task started: CheckM
[2024-01-24 13:46:39,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704555.1_ASM870455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704555.1_ASM870455v1_genomic.fna/checkm_input GCF_008704555.1_ASM870455v1_genomic.fna/checkm_result
[2024-01-24 13:48:39,106] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:39,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:39,136] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:39,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:39,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704555.1_ASM870455v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:39,138] [INFO] Task started: Blastn
[2024-01-24 13:48:39,139] [INFO] Running command: blastn -query GCF_008704555.1_ASM870455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ded479-50a3-4de5-ae87-119e4e7b51fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704555.1_ASM870455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:41,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:41,128] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:41,128] [INFO] Target genome list was writen to GCF_008704555.1_ASM870455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:41,147] [INFO] Task started: fastANI
[2024-01-24 13:48:41,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg889636f1-eabb-4425-8689-b4455dce0fbd/GCF_008704555.1_ASM870455v1_genomic.fna.gz --refList GCF_008704555.1_ASM870455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704555.1_ASM870455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:02,317] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:02,331] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:02,332] [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_008704555.1	s__Streptomyces nitrosporeus	100.0	2527	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCF_000177195.2	s__Streptomyces sp000177195	87.5868	1696	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.71	97.52	0.98	0.91	17	-
GCA_000720535.1	s__Streptomyces halstedii	87.2295	1731	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	96.54	0.92	0.83	17	-
GCF_002711365.1	s__Streptomyces sp002711365	86.2422	1684	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	-
GCF_001905505.1	s__Streptomyces sp001905505	86.0437	1722	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001715295.1	s__Streptomyces griseus_G	86.0082	1534	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014651175.1	s__Streptomyces clavifer	85.9573	1702	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	-
GCF_002941025.1	s__Streptomyces sp002941025	85.9459	1739	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829855.1	s__Streptomyces argenteolus	85.7878	1694	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717025.1	s__Streptomyces atroolivaceus	85.6325	1698	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905735.1	s__Streptomyces sp001905735	84.1532	1519	2527	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	95.22	0.92	0.85	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:02,334] [INFO] GTDB search result was written to GCF_008704555.1_ASM870455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:02,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:02,342] [INFO] DFAST_QC result json was written to GCF_008704555.1_ASM870455v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:02,342] [INFO] DFAST_QC completed!
[2024-01-24 13:49:02,342] [INFO] Total running time: 0h3m14s