[2024-01-24 13:26:10,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:10,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:10,112] [INFO] DQC Reference Directory: /var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference
[2024-01-24 13:26:11,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:11,330] [INFO] Task started: Prodigal
[2024-01-24 13:26:11,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg612c1a01-b4b5-40ce-ba6e-4f29a476ec61/GCF_000243395.2_ASM24339v3_genomic.fna.gz | prodigal -d GCF_000243395.2_ASM24339v3_genomic.fna/cds.fna -a GCF_000243395.2_ASM24339v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:26,305] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:26,305] [INFO] Task started: HMMsearch
[2024-01-24 13:26:26,306] [INFO] Running command: hmmsearch --tblout GCF_000243395.2_ASM24339v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference/reference_markers.hmm GCF_000243395.2_ASM24339v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:26,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:26,603] [INFO] Found 6/6 markers.
[2024-01-24 13:26:26,645] [INFO] Query marker FASTA was written to GCF_000243395.2_ASM24339v3_genomic.fna/markers.fasta
[2024-01-24 13:26:26,646] [INFO] Task started: Blastn
[2024-01-24 13:26:26,646] [INFO] Running command: blastn -query GCF_000243395.2_ASM24339v3_genomic.fna/markers.fasta -db /var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference/reference_markers.fasta -out GCF_000243395.2_ASM24339v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:27,916] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:27,920] [INFO] Selected 16 target genomes.
[2024-01-24 13:26:27,921] [INFO] Target genome list was writen to GCF_000243395.2_ASM24339v3_genomic.fna/target_genomes.txt
[2024-01-24 13:26:27,955] [INFO] Task started: fastANI
[2024-01-24 13:26:27,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg612c1a01-b4b5-40ce-ba6e-4f29a476ec61/GCF_000243395.2_ASM24339v3_genomic.fna.gz --refList GCF_000243395.2_ASM24339v3_genomic.fna/target_genomes.txt --output GCF_000243395.2_ASM24339v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:46,775] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:46,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:46,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:46,802] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:46,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:46,802] [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
Saccharomonospora glauca	strain=K62	GCA_000243395.3	40990	40990	type	True	100.0	1519	1520	95	conclusive
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	89.0028	1285	1520	95	below_threshold
Saccharomonospora azurea	strain=NA-128	GCA_000231055.3	40988	40988	type	True	85.3447	1162	1520	95	below_threshold
Saccharomonospora xinjiangensis	strain=XJ-54	GCA_000258175.1	75294	75294	type	True	84.0844	1093	1520	95	below_threshold
Saccharomonospora viridis	strain=DSM 43017	GCA_000023865.1	1852	1852	type	True	82.8065	982	1520	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	81.9886	1002	1520	95	below_threshold
Saccharomonospora saliphila	strain=YIM 90502	GCA_000383795.1	369829	369829	type	True	80.667	706	1520	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.9186	794	1520	95	below_threshold
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	79.2269	635	1520	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7826	647	1520	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.3302	654	1520	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.9715	475	1520	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	77.9447	518	1520	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	77.9077	510	1520	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	77.3411	288	1520	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	76.523	289	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:46,804] [INFO] DFAST Taxonomy check result was written to GCF_000243395.2_ASM24339v3_genomic.fna/tc_result.tsv
[2024-01-24 13:26:46,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:46,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:46,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference/checkm_data
[2024-01-24 13:26:46,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:46,879] [INFO] Task started: CheckM
[2024-01-24 13:26:46,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243395.2_ASM24339v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243395.2_ASM24339v3_genomic.fna/checkm_input GCF_000243395.2_ASM24339v3_genomic.fna/checkm_result
[2024-01-24 13:27:46,518] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:46,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:46,543] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:46,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:46,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243395.2_ASM24339v3_genomic.fna/markers.fasta)
[2024-01-24 13:27:46,544] [INFO] Task started: Blastn
[2024-01-24 13:27:46,545] [INFO] Running command: blastn -query GCF_000243395.2_ASM24339v3_genomic.fna/markers.fasta -db /var/lib/cwl/stga3602505-843a-4a91-9e94-af463ec38dce/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243395.2_ASM24339v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:48,467] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:48,471] [INFO] Selected 11 target genomes.
[2024-01-24 13:27:48,471] [INFO] Target genome list was writen to GCF_000243395.2_ASM24339v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:48,528] [INFO] Task started: fastANI
[2024-01-24 13:27:48,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg612c1a01-b4b5-40ce-ba6e-4f29a476ec61/GCF_000243395.2_ASM24339v3_genomic.fna.gz --refList GCF_000243395.2_ASM24339v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000243395.2_ASM24339v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:00,650] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:00,664] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:00,664] [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_000243395.2	s__Saccharomonospora glauca	100.0	1519	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000244975.1	s__Saccharomonospora cyanea	88.9889	1286	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231055.2	s__Saccharomonospora azurea	85.324	1164	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.11	99.11	0.89	0.89	2	-
GCF_015910535.1	s__Saccharomonospora sp015910535	84.3824	1090	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258175.1	s__Saccharomonospora xinjiangensis	84.0493	1097	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	96.93	96.93	0.94	0.94	2	-
GCF_000023865.1	s__Saccharomonospora viridis	82.7696	984	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.62	99.61	0.97	0.97	3	-
GCF_005862235.1	s__Saccharomonospora piscinae	81.9712	1004	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_000383795.1	s__Saccharomonospora saliphila	80.6674	706	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405885.1	s__Gandjariella thermophila	77.8177	460	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362825.1	s__Labedaea rhizosphaerae	77.7268	526	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408175.1	s__Actinopolyspora biskrensis	77.3158	289	1520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:00,666] [INFO] GTDB search result was written to GCF_000243395.2_ASM24339v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:00,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:00,670] [INFO] DFAST_QC result json was written to GCF_000243395.2_ASM24339v3_genomic.fna/dqc_result.json
[2024-01-24 13:28:00,670] [INFO] DFAST_QC completed!
[2024-01-24 13:28:00,670] [INFO] Total running time: 0h1m51s