[2024-01-25 18:53:05,650] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference
[2024-01-25 18:53:06,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:06,795] [INFO] Task started: Prodigal
[2024-01-25 18:53:06,795] [INFO] Running command: gunzip -c /var/lib/cwl/stgf03243a4-6760-4b75-b55f-c8a338ac0caf/GCF_024172085.1_ASM2417208v1_genomic.fna.gz | prodigal -d GCF_024172085.1_ASM2417208v1_genomic.fna/cds.fna -a GCF_024172085.1_ASM2417208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:29,411] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:29,411] [INFO] Task started: HMMsearch
[2024-01-25 18:53:29,411] [INFO] Running command: hmmsearch --tblout GCF_024172085.1_ASM2417208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference/reference_markers.hmm GCF_024172085.1_ASM2417208v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:29,833] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:29,834] [INFO] Found 6/6 markers.
[2024-01-25 18:53:29,913] [INFO] Query marker FASTA was written to GCF_024172085.1_ASM2417208v1_genomic.fna/markers.fasta
[2024-01-25 18:53:29,914] [INFO] Task started: Blastn
[2024-01-25 18:53:29,914] [INFO] Running command: blastn -query GCF_024172085.1_ASM2417208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference/reference_markers.fasta -out GCF_024172085.1_ASM2417208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:31,072] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:31,075] [INFO] Selected 20 target genomes.
[2024-01-25 18:53:31,076] [INFO] Target genome list was writen to GCF_024172085.1_ASM2417208v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:31,102] [INFO] Task started: fastANI
[2024-01-25 18:53:31,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgf03243a4-6760-4b75-b55f-c8a338ac0caf/GCF_024172085.1_ASM2417208v1_genomic.fna.gz --refList GCF_024172085.1_ASM2417208v1_genomic.fna/target_genomes.txt --output GCF_024172085.1_ASM2417208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:03,847] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:03,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:03,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:03,861] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:54:03,862] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:54:03,862] [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
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	78.8189	1124	2954	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	78.6831	1181	2954	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	78.6537	1171	2954	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	78.629	1162	2954	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	78.5839	1106	2954	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	78.5478	722	2954	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	78.5227	1098	2954	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	78.4995	1180	2954	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	78.477	958	2954	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	78.4443	917	2954	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	78.3942	939	2954	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	78.2998	923	2954	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.2603	808	2954	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	78.199	965	2954	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	78.1918	976	2954	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	78.1889	930	2954	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	78.1062	863	2954	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	78.0087	796	2954	95	below_threshold
Rhizocola hellebori	strain=NBRC 109834	GCA_016862955.1	1392758	1392758	type	True	77.6756	725	2954	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	77.308	1125	2954	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:03,863] [INFO] DFAST Taxonomy check result was written to GCF_024172085.1_ASM2417208v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:03,864] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:03,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:03,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference/checkm_data
[2024-01-25 18:54:03,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:03,951] [INFO] Task started: CheckM
[2024-01-25 18:54:03,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172085.1_ASM2417208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172085.1_ASM2417208v1_genomic.fna/checkm_input GCF_024172085.1_ASM2417208v1_genomic.fna/checkm_result
[2024-01-25 18:55:27,466] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:27,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:27,487] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:27,487] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:27,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172085.1_ASM2417208v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:27,488] [INFO] Task started: Blastn
[2024-01-25 18:55:27,488] [INFO] Running command: blastn -query GCF_024172085.1_ASM2417208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2535f7ab-dd34-4906-919b-0a8370fadfc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172085.1_ASM2417208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:29,276] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:29,279] [INFO] Selected 16 target genomes.
[2024-01-25 18:55:29,279] [INFO] Target genome list was writen to GCF_024172085.1_ASM2417208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:29,294] [INFO] Task started: fastANI
[2024-01-25 18:55:29,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgf03243a4-6760-4b75-b55f-c8a338ac0caf/GCF_024172085.1_ASM2417208v1_genomic.fna.gz --refList GCF_024172085.1_ASM2417208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172085.1_ASM2417208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:58,479] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:58,489] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:55:58,489] [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
GCA_013361475.1	s__Hamadaea sp013361475	89.7745	1638	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	99.33	99.31	0.83	0.82	3	-
GCA_013362815.1	s__Hamadaea sp013362815	87.8858	1948	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428945.1	s__Hamadaea tsunoensis	80.8264	1485	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	79.0097	1162	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCF_016862635.1	s__Catellatospora coxensis	78.8846	1139	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204945.1	s__Allocatelliglobosispora scoriae	78.8589	1097	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allocatelliglobosispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083965.1	s__Catellatospora sp019083965	78.8134	1127	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018327705.1	s__Catellatospora sp018327705	78.7442	1199	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720365.1	s__Catellatospora paridis	78.6066	1168	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	78.5841	715	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011297335.1	s__Catellatospora methionotrophica	78.5823	1107	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009720385.1	s__Catellatospora vulcania	78.484	1186	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002926165.1	s__Micromonospora chalcea	78.2601	936	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_003172955.1	s__Micromonospora sp003172955	78.2284	815	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907275.1	s__Micromonospora luteifusca	77.9932	801	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	77.7403	1005	2954	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:58,490] [INFO] GTDB search result was written to GCF_024172085.1_ASM2417208v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:58,491] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:58,494] [INFO] DFAST_QC result json was written to GCF_024172085.1_ASM2417208v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:58,494] [INFO] DFAST_QC completed!
[2024-01-25 18:55:58,494] [INFO] Total running time: 0h2m53s