[2024-01-24 13:31:27,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:27,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:27,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference
[2024-01-24 13:31:29,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:29,220] [INFO] Task started: Prodigal
[2024-01-24 13:31:29,220] [INFO] Running command: gunzip -c /var/lib/cwl/stg081eb626-4ca4-4903-9d1e-3c93b843c835/GCF_009829685.1_ASM982968v1_genomic.fna.gz | prodigal -d GCF_009829685.1_ASM982968v1_genomic.fna/cds.fna -a GCF_009829685.1_ASM982968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:37,977] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:37,977] [INFO] Task started: HMMsearch
[2024-01-24 13:31:37,977] [INFO] Running command: hmmsearch --tblout GCF_009829685.1_ASM982968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference/reference_markers.hmm GCF_009829685.1_ASM982968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:38,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:38,261] [INFO] Found 6/6 markers.
[2024-01-24 13:31:38,294] [INFO] Query marker FASTA was written to GCF_009829685.1_ASM982968v1_genomic.fna/markers.fasta
[2024-01-24 13:31:38,294] [INFO] Task started: Blastn
[2024-01-24 13:31:38,295] [INFO] Running command: blastn -query GCF_009829685.1_ASM982968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference/reference_markers.fasta -out GCF_009829685.1_ASM982968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:39,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:39,724] [INFO] Selected 24 target genomes.
[2024-01-24 13:31:39,725] [INFO] Target genome list was writen to GCF_009829685.1_ASM982968v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:39,734] [INFO] Task started: fastANI
[2024-01-24 13:31:39,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg081eb626-4ca4-4903-9d1e-3c93b843c835/GCF_009829685.1_ASM982968v1_genomic.fna.gz --refList GCF_009829685.1_ASM982968v1_genomic.fna/target_genomes.txt --output GCF_009829685.1_ASM982968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:57,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:57,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:57,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:57,848] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:57,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:57,849] [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
Cellulomonas citrea	strain=Ao-9	GCA_009829685.1	1909423	1909423	type	True	100.0	940	949	95	conclusive
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	80.1113	530	949	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	79.9118	460	949	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	79.8512	483	949	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.8415	473	949	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	79.8225	466	949	95	below_threshold
Cellulomonas composti	strain=NBRC 100758	GCA_007990245.1	266130	266130	type	True	79.8151	460	949	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	79.7855	528	949	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	79.7602	478	949	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	79.7586	511	949	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	79.7526	440	949	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	79.7522	519	949	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	79.7248	518	949	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	79.6888	459	949	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	79.6822	510	949	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.6306	522	949	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.5972	473	949	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.5313	487	949	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	79.5287	497	949	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	79.4503	491	949	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	79.1057	460	949	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	78.9323	364	949	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	78.4729	363	949	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.4503	376	949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:57,851] [INFO] DFAST Taxonomy check result was written to GCF_009829685.1_ASM982968v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:57,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:57,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:57,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference/checkm_data
[2024-01-24 13:31:57,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:57,886] [INFO] Task started: CheckM
[2024-01-24 13:31:57,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009829685.1_ASM982968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009829685.1_ASM982968v1_genomic.fna/checkm_input GCF_009829685.1_ASM982968v1_genomic.fna/checkm_result
[2024-01-24 13:32:48,551] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:48,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:48,576] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:48,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:48,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009829685.1_ASM982968v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:48,577] [INFO] Task started: Blastn
[2024-01-24 13:32:48,578] [INFO] Running command: blastn -query GCF_009829685.1_ASM982968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1729a214-f4f6-406b-bee2-432fd44be579/dqc_reference/reference_markers_gtdb.fasta -out GCF_009829685.1_ASM982968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:50,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:50,863] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:50,864] [INFO] Target genome list was writen to GCF_009829685.1_ASM982968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:50,883] [INFO] Task started: fastANI
[2024-01-24 13:32:50,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg081eb626-4ca4-4903-9d1e-3c93b843c835/GCF_009829685.1_ASM982968v1_genomic.fna.gz --refList GCF_009829685.1_ASM982968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009829685.1_ASM982968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:10,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,167] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:10,168] [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_009829685.1	s__Cellulomonas citrea	100.0	940	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018898235.1	s__Cellulomonas sp018898235	85.2507	555	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009785115.1	s__Cellulomonas sp009785115	80.1413	379	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409305.1	s__Cellulomonas soli	80.1107	530	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011603975.1	s__Cellulomonas sp011603975	79.9902	450	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218545.1	s__Cellulomonas gilvus	79.91	461	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386485.1	s__Cellulomonas oligotrophica	79.7885	530	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	79.7829	437	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388445.1	s__Cellulomonas sp018388445	79.7732	497	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	79.7553	472	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001552375.1	s__Cellulomonas iranensis	79.7521	514	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_008033115.1	s__Cellulomonas sp008033115	79.7396	521	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_016862775.1	s__Cellulomonas phragmiteti	79.7261	483	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003755175.1	s__Cellulomonas sp003755175	79.7029	474	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114185.1	s__Cellulomonas sp900114185	79.6804	504	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836445.1	s__Cellulomonas sp014836445	79.6515	468	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	79.6301	532	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531375.1	s__Cellulomonas sp018531375	79.5944	481	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092865.1	s__Cellulomonas flavigena	79.5538	494	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862675.1	s__Cellulomonas chitinilytica	79.5113	520	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	79.4747	489	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744555.1	s__Cellulomonas sp017744555	79.3781	468	949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,169] [INFO] GTDB search result was written to GCF_009829685.1_ASM982968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:10,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:10,174] [INFO] DFAST_QC result json was written to GCF_009829685.1_ASM982968v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:10,174] [INFO] DFAST_QC completed!
[2024-01-24 13:33:10,174] [INFO] Total running time: 0h1m42s