[2024-01-24 13:55:12,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:12,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:12,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference
[2024-01-24 13:55:13,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:13,428] [INFO] Task started: Prodigal
[2024-01-24 13:55:13,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d6d0ddd-f251-4da3-b5a3-9ba6e46666ed/GCF_000384035.1_ASM38403v1_genomic.fna.gz | prodigal -d GCF_000384035.1_ASM38403v1_genomic.fna/cds.fna -a GCF_000384035.1_ASM38403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:26,751] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:26,751] [INFO] Task started: HMMsearch
[2024-01-24 13:55:26,751] [INFO] Running command: hmmsearch --tblout GCF_000384035.1_ASM38403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference/reference_markers.hmm GCF_000384035.1_ASM38403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:27,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:27,018] [INFO] Found 6/6 markers.
[2024-01-24 13:55:27,059] [INFO] Query marker FASTA was written to GCF_000384035.1_ASM38403v1_genomic.fna/markers.fasta
[2024-01-24 13:55:27,059] [INFO] Task started: Blastn
[2024-01-24 13:55:27,059] [INFO] Running command: blastn -query GCF_000384035.1_ASM38403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference/reference_markers.fasta -out GCF_000384035.1_ASM38403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:28,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:28,146] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:28,147] [INFO] Target genome list was writen to GCF_000384035.1_ASM38403v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:28,170] [INFO] Task started: fastANI
[2024-01-24 13:55:28,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6d0ddd-f251-4da3-b5a3-9ba6e46666ed/GCF_000384035.1_ASM38403v1_genomic.fna.gz --refList GCF_000384035.1_ASM38403v1_genomic.fna/target_genomes.txt --output GCF_000384035.1_ASM38403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:40,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:40,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:40,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:40,686] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:40,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:40,687] [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
Actinopolyspora mortivallis	strain=HS-1	GCA_000384035.1	33906	33906	type	True	100.0	1410	1411	95	conclusive
Actinopolyspora saharensis	strain=DSM 45459	GCA_900100925.1	995062	995062	type	True	83.3846	1039	1411	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	83.1396	1029	1411	95	below_threshold
Actinopolyspora halophila	strain=DSM 43834	GCA_000371785.1	1850	1850	type	True	82.9105	1040	1411	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	81.9803	969	1411	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	81.9109	967	1411	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	81.8853	952	1411	95	below_threshold
Actinopolyspora alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	81.5705	920	1411	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	81.2276	912	1411	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	79.0858	595	1411	95	below_threshold
Saccharopolyspora dendranthemae	strain=DSM 46699	GCA_007829955.1	1181886	1181886	type	True	78.6049	536	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:40,689] [INFO] DFAST Taxonomy check result was written to GCF_000384035.1_ASM38403v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:40,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:40,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:40,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference/checkm_data
[2024-01-24 13:55:40,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:40,746] [INFO] Task started: CheckM
[2024-01-24 13:55:40,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000384035.1_ASM38403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000384035.1_ASM38403v1_genomic.fna/checkm_input GCF_000384035.1_ASM38403v1_genomic.fna/checkm_result
[2024-01-24 13:56:36,115] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:36,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:36,138] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:36,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:36,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000384035.1_ASM38403v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:36,139] [INFO] Task started: Blastn
[2024-01-24 13:56:36,139] [INFO] Running command: blastn -query GCF_000384035.1_ASM38403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3504e63c-2487-4e56-a667-3c69c6649bdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000384035.1_ASM38403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:37,804] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:37,808] [INFO] Selected 10 target genomes.
[2024-01-24 13:56:37,809] [INFO] Target genome list was writen to GCF_000384035.1_ASM38403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:37,820] [INFO] Task started: fastANI
[2024-01-24 13:56:37,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6d0ddd-f251-4da3-b5a3-9ba6e46666ed/GCF_000384035.1_ASM38403v1_genomic.fna.gz --refList GCF_000384035.1_ASM38403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000384035.1_ASM38403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:48,993] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:49,006] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:49,006] [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_000384035.1	s__Actinopolyspora mortivallis	100.0	1410	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	95.34	95.34	0.86	0.86	2	conclusive
GCF_900100925.1	s__Actinopolyspora saharensis	83.3915	1038	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_013408175.1	s__Actinopolyspora biskrensis	83.1602	1026	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716775.1	s__Actinopolyspora sp006716775	83.0316	1022	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000371785.1	s__Actinopolyspora halophila	82.9027	1041	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263515.1	s__Actinopolyspora erythraea	81.9832	969	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900104475.1	s__Actinopolyspora xinjiangensis	81.8766	955	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112765.1	s__Actinopolyspora alba	81.5445	924	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	N/A	N/A	N/A	N/A	1	-
GCF_900116555.1	s__Actinopolyspora righensis	81.2377	910	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
GCF_013410345.1	s__Saccharopolyspora hordei	79.0916	599	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:49,008] [INFO] GTDB search result was written to GCF_000384035.1_ASM38403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:49,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:49,013] [INFO] DFAST_QC result json was written to GCF_000384035.1_ASM38403v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:49,013] [INFO] DFAST_QC completed!
[2024-01-24 13:56:49,013] [INFO] Total running time: 0h1m37s