[2024-01-25 20:02:05,812] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference
[2024-01-25 20:02:07,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:07,042] [INFO] Task started: Prodigal
[2024-01-25 20:02:07,043] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa26d0b1-2288-44a5-8890-29f76b4c5329/GCF_014837295.1_ASM1483729v1_genomic.fna.gz | prodigal -d GCF_014837295.1_ASM1483729v1_genomic.fna/cds.fna -a GCF_014837295.1_ASM1483729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:16,556] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:16,557] [INFO] Task started: HMMsearch
[2024-01-25 20:02:16,557] [INFO] Running command: hmmsearch --tblout GCF_014837295.1_ASM1483729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference/reference_markers.hmm GCF_014837295.1_ASM1483729v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:16,779] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:16,780] [INFO] Found 6/6 markers.
[2024-01-25 20:02:16,811] [INFO] Query marker FASTA was written to GCF_014837295.1_ASM1483729v1_genomic.fna/markers.fasta
[2024-01-25 20:02:16,812] [INFO] Task started: Blastn
[2024-01-25 20:02:16,812] [INFO] Running command: blastn -query GCF_014837295.1_ASM1483729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference/reference_markers.fasta -out GCF_014837295.1_ASM1483729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:18,010] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:18,013] [INFO] Selected 16 target genomes.
[2024-01-25 20:02:18,014] [INFO] Target genome list was writen to GCF_014837295.1_ASM1483729v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:18,027] [INFO] Task started: fastANI
[2024-01-25 20:02:18,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa26d0b1-2288-44a5-8890-29f76b4c5329/GCF_014837295.1_ASM1483729v1_genomic.fna.gz --refList GCF_014837295.1_ASM1483729v1_genomic.fna/target_genomes.txt --output GCF_014837295.1_ASM1483729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:34,263] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:34,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:34,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:34,274] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:34,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:34,274] [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
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	100.0	1299	1300	95	conclusive
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	83.5424	909	1300	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	83.5183	889	1300	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	83.36	904	1300	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	80.6862	738	1300	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	80.6698	723	1300	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	80.5775	728	1300	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	80.5657	672	1300	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	80.507	676	1300	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	80.5051	721	1300	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	79.3658	606	1300	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	79.1181	551	1300	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.8525	588	1300	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.6434	608	1300	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	77.1009	270	1300	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	75.9505	327	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:34,276] [INFO] DFAST Taxonomy check result was written to GCF_014837295.1_ASM1483729v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:34,276] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:34,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:34,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference/checkm_data
[2024-01-25 20:02:34,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:34,317] [INFO] Task started: CheckM
[2024-01-25 20:02:34,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837295.1_ASM1483729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837295.1_ASM1483729v1_genomic.fna/checkm_input GCF_014837295.1_ASM1483729v1_genomic.fna/checkm_result
[2024-01-25 20:03:27,528] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:27,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:27,541] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:27,541] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:27,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837295.1_ASM1483729v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:27,542] [INFO] Task started: Blastn
[2024-01-25 20:03:27,542] [INFO] Running command: blastn -query GCF_014837295.1_ASM1483729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg708cda27-eef6-4a24-8159-d6a69632e272/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837295.1_ASM1483729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:29,464] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:29,467] [INFO] Selected 21 target genomes.
[2024-01-25 20:03:29,467] [INFO] Target genome list was writen to GCF_014837295.1_ASM1483729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:29,490] [INFO] Task started: fastANI
[2024-01-25 20:03:29,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa26d0b1-2288-44a5-8890-29f76b4c5329/GCF_014837295.1_ASM1483729v1_genomic.fna.gz --refList GCF_014837295.1_ASM1483729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837295.1_ASM1483729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:49,968] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:49,980] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:49,981] [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_014837295.1	s__Cellulosimicrobium arenosum	100.0	1299	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014803435.1	s__Cellulosimicrobium terreum	85.2887	1056	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	83.7556	757	1300	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	83.7076	907	1300	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	83.63	988	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	83.5914	952	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_004519295.1	s__Cellulosimicrobium funkei	83.5559	908	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	83.5272	953	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	83.5022	964	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	83.4663	939	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	83.4313	876	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907365.1	s__Oerskovia paurometabola	80.6873	732	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_000215105.1	s__Isoptericola variabilis_A	80.6313	637	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_014836755.1	s__Oerskovia sp014836755	80.5654	730	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752595.1	s__Sediminihabitans sp003752595	80.1036	635	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	79.343	609	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216535.1	s__Xylanimonas ulmi	79.3212	547	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	79.0837	507	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	79.0368	524	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892515.1	s__Myceligenerans sp014892515	78.9774	543	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_016862755.1	s__Cellulomonas pakistanensis	78.885	580	1300	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:49,982] [INFO] GTDB search result was written to GCF_014837295.1_ASM1483729v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:49,983] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:49,987] [INFO] DFAST_QC result json was written to GCF_014837295.1_ASM1483729v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:49,988] [INFO] DFAST_QC completed!
[2024-01-25 20:03:49,988] [INFO] Total running time: 0h1m44s