[2024-01-24 14:14:47,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference
[2024-01-24 14:14:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,423] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,423] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6dceeae-d44b-4807-a466-faae51552fc4/GCF_005862235.1_ASM586223v1_genomic.fna.gz | prodigal -d GCF_005862235.1_ASM586223v1_genomic.fna/cds.fna -a GCF_005862235.1_ASM586223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:05,097] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:05,097] [INFO] Task started: HMMsearch
[2024-01-24 14:15:05,097] [INFO] Running command: hmmsearch --tblout GCF_005862235.1_ASM586223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference/reference_markers.hmm GCF_005862235.1_ASM586223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:05,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:05,437] [INFO] Found 6/6 markers.
[2024-01-24 14:15:05,480] [INFO] Query marker FASTA was written to GCF_005862235.1_ASM586223v1_genomic.fna/markers.fasta
[2024-01-24 14:15:05,481] [INFO] Task started: Blastn
[2024-01-24 14:15:05,481] [INFO] Running command: blastn -query GCF_005862235.1_ASM586223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference/reference_markers.fasta -out GCF_005862235.1_ASM586223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:06,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:06,864] [INFO] Selected 16 target genomes.
[2024-01-24 14:15:06,865] [INFO] Target genome list was writen to GCF_005862235.1_ASM586223v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:06,874] [INFO] Task started: fastANI
[2024-01-24 14:15:06,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6dceeae-d44b-4807-a466-faae51552fc4/GCF_005862235.1_ASM586223v1_genomic.fna.gz --refList GCF_005862235.1_ASM586223v1_genomic.fna/target_genomes.txt --output GCF_005862235.1_ASM586223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:27,277] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:27,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:27,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:27,292] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:27,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:27,293] [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 piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	100.0	1628	1628	95	conclusive
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	82.6701	1087	1628	95	below_threshold
Saccharomonospora azurea	strain=NA-128	GCA_000231055.3	40988	40988	type	True	82.1818	1057	1628	95	below_threshold
Saccharomonospora glauca	strain=K62	GCA_000243395.3	40990	40990	type	True	81.9403	1018	1628	95	below_threshold
Saccharomonospora xinjiangensis	strain=XJ-54	GCA_000258175.1	75294	75294	type	True	81.7352	1031	1628	95	below_threshold
Saccharomonospora viridis	strain=DSM 43017	GCA_000023865.1	1852	1852	type	True	81.3437	909	1628	95	below_threshold
Saccharomonospora saliphila	strain=YIM 90502	GCA_000383795.1	369829	369829	type	True	81.0026	792	1628	95	below_threshold
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	80.8203	709	1628	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	80.6342	817	1628	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.4022	884	1628	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.5835	796	1628	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.5244	810	1628	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.9453	766	1628	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.4971	766	1628	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.0437	561	1628	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	76.4943	324	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:27,294] [INFO] DFAST Taxonomy check result was written to GCF_005862235.1_ASM586223v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:27,295] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:27,295] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:27,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference/checkm_data
[2024-01-24 14:15:27,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:27,345] [INFO] Task started: CheckM
[2024-01-24 14:15:27,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005862235.1_ASM586223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005862235.1_ASM586223v1_genomic.fna/checkm_input GCF_005862235.1_ASM586223v1_genomic.fna/checkm_result
[2024-01-24 14:16:25,785] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:25,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:25,807] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:25,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:25,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005862235.1_ASM586223v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:25,808] [INFO] Task started: Blastn
[2024-01-24 14:16:25,808] [INFO] Running command: blastn -query GCF_005862235.1_ASM586223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg679d7c8d-f50e-4f88-91c8-16746d2a401b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005862235.1_ASM586223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:27,713] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:27,718] [INFO] Selected 10 target genomes.
[2024-01-24 14:16:27,718] [INFO] Target genome list was writen to GCF_005862235.1_ASM586223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:27,726] [INFO] Task started: fastANI
[2024-01-24 14:16:27,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6dceeae-d44b-4807-a466-faae51552fc4/GCF_005862235.1_ASM586223v1_genomic.fna.gz --refList GCF_005862235.1_ASM586223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005862235.1_ASM586223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:39,442] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:39,458] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:39,459] [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_005862235.1	s__Saccharomonospora piscinae	100.0	1628	1628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	conclusive
GCF_000244975.1	s__Saccharomonospora cyanea	82.6575	1089	1628	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	82.1818	1057	1628	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	82.0159	974	1628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243395.2	s__Saccharomonospora glauca	81.9693	1014	1628	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	81.7202	1033	1628	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	81.3286	911	1628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.62	99.61	0.97	0.97	3	-
GCF_000430445.1	s__Saccharomonospora iraqiensis	80.8197	709	1628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_000231035.2	s__Saccharomonospora paurometabolica	80.6319	817	1628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	96.0038	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	79.5862	793	1628	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:39,460] [INFO] GTDB search result was written to GCF_005862235.1_ASM586223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:39,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:39,464] [INFO] DFAST_QC result json was written to GCF_005862235.1_ASM586223v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:39,465] [INFO] DFAST_QC completed!
[2024-01-24 14:16:39,465] [INFO] Total running time: 0h1m52s