[2024-01-24 12:13:27,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference
[2024-01-24 12:13:29,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,402] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,402] [INFO] Running command: gunzip -c /var/lib/cwl/stgf87438ec-fda1-41b0-a2a4-02060f66a872/GCF_000024925.1_ASM2492v1_genomic.fna.gz | prodigal -d GCF_000024925.1_ASM2492v1_genomic.fna/cds.fna -a GCF_000024925.1_ASM2492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:41,762] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:41,762] [INFO] Task started: HMMsearch
[2024-01-24 12:13:41,762] [INFO] Running command: hmmsearch --tblout GCF_000024925.1_ASM2492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference/reference_markers.hmm GCF_000024925.1_ASM2492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:42,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:42,082] [INFO] Found 6/6 markers.
[2024-01-24 12:13:42,127] [INFO] Query marker FASTA was written to GCF_000024925.1_ASM2492v1_genomic.fna/markers.fasta
[2024-01-24 12:13:42,127] [INFO] Task started: Blastn
[2024-01-24 12:13:42,127] [INFO] Running command: blastn -query GCF_000024925.1_ASM2492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference/reference_markers.fasta -out GCF_000024925.1_ASM2492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:43,543] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:43,547] [INFO] Selected 18 target genomes.
[2024-01-24 12:13:43,548] [INFO] Target genome list was writen to GCF_000024925.1_ASM2492v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:43,557] [INFO] Task started: fastANI
[2024-01-24 12:13:43,557] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87438ec-fda1-41b0-a2a4-02060f66a872/GCF_000024925.1_ASM2492v1_genomic.fna.gz --refList GCF_000024925.1_ASM2492v1_genomic.fna/target_genomes.txt --output GCF_000024925.1_ASM2492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:59,623] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:59,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:59,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:59,637] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:59,637] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:59,638] [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
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	100.0	1416	1417	95	conclusive
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	86.7398	1078	1417	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	81.7198	746	1417	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	81.4856	727	1417	95	below_threshold
Sanguibacter suaedae	strain=YZGR15	GCA_016342785.1	2795737	2795737	type	True	81.0847	632	1417	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	80.406	613	1417	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.9691	593	1417	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.9559	604	1417	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.8454	629	1417	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.7956	615	1417	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.9432	573	1417	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	78.9064	551	1417	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	78.854	561	1417	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.8189	545	1417	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.7293	611	1417	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.7113	586	1417	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.6832	514	1417	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.6121	516	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:59,639] [INFO] DFAST Taxonomy check result was written to GCF_000024925.1_ASM2492v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:59,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:59,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:59,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference/checkm_data
[2024-01-24 12:13:59,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:59,683] [INFO] Task started: CheckM
[2024-01-24 12:13:59,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024925.1_ASM2492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024925.1_ASM2492v1_genomic.fna/checkm_input GCF_000024925.1_ASM2492v1_genomic.fna/checkm_result
[2024-01-24 12:15:14,729] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:14,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:14,749] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:14,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:14,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024925.1_ASM2492v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:14,751] [INFO] Task started: Blastn
[2024-01-24 12:15:14,751] [INFO] Running command: blastn -query GCF_000024925.1_ASM2492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dab39d5-5d90-4afb-a5a7-f8fe598fbeb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024925.1_ASM2492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:16,845] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:16,849] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:16,849] [INFO] Target genome list was writen to GCF_000024925.1_ASM2492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:16,868] [INFO] Task started: fastANI
[2024-01-24 12:15:16,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87438ec-fda1-41b0-a2a4-02060f66a872/GCF_000024925.1_ASM2492v1_genomic.fna.gz --refList GCF_000024925.1_ASM2492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024925.1_ASM2492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:31,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:31,871] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:31,872] [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_000024925.1	s__Sanguibacter keddieii	100.0	1416	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013415325.1	s__Sanguibacter inulinus	86.7467	1077	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
GCF_001552735.1	s__Sanguibacter suarezii	81.7357	744	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096585.1	s__Sanguibacter gelidistatuariae	81.4782	727	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016342785.1	s__Sanguibacter sp016342785	81.1192	629	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564005.1	s__Sanguibacter antarcticus	80.3946	613	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	79.5553	536	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	79.466	596	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	79.4545	644	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	79.1455	496	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	79.05	635	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_001462455.1	s__Cellulomonas sp001462455	79.0237	553	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	78.9536	534	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464425.1	s__Actinotalea solisilvae	78.9357	574	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	78.6994	517	1417	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	78.3968	546	1417	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 12:15:31,873] [INFO] GTDB search result was written to GCF_000024925.1_ASM2492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:31,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:31,878] [INFO] DFAST_QC result json was written to GCF_000024925.1_ASM2492v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:31,878] [INFO] DFAST_QC completed!
[2024-01-24 12:15:31,878] [INFO] Total running time: 0h2m4s