[2024-01-24 11:26:28,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,293] [INFO] DQC Reference Directory: /var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference
[2024-01-24 11:26:29,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,630] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg0edd6e16-cfd9-4bdd-9c7f-5a344db9364c/GCF_002563925.1_ASM256392v1_genomic.fna.gz | prodigal -d GCF_002563925.1_ASM256392v1_genomic.fna/cds.fna -a GCF_002563925.1_ASM256392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:39,916] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:39,916] [INFO] Task started: HMMsearch
[2024-01-24 11:26:39,916] [INFO] Running command: hmmsearch --tblout GCF_002563925.1_ASM256392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference/reference_markers.hmm GCF_002563925.1_ASM256392v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:40,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:40,197] [INFO] Found 6/6 markers.
[2024-01-24 11:26:40,224] [INFO] Query marker FASTA was written to GCF_002563925.1_ASM256392v1_genomic.fna/markers.fasta
[2024-01-24 11:26:40,224] [INFO] Task started: Blastn
[2024-01-24 11:26:40,225] [INFO] Running command: blastn -query GCF_002563925.1_ASM256392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference/reference_markers.fasta -out GCF_002563925.1_ASM256392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:41,328] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:41,331] [INFO] Selected 29 target genomes.
[2024-01-24 11:26:41,331] [INFO] Target genome list was writen to GCF_002563925.1_ASM256392v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:41,341] [INFO] Task started: fastANI
[2024-01-24 11:26:41,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg0edd6e16-cfd9-4bdd-9c7f-5a344db9364c/GCF_002563925.1_ASM256392v1_genomic.fna.gz --refList GCF_002563925.1_ASM256392v1_genomic.fna/target_genomes.txt --output GCF_002563925.1_ASM256392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:02,768] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:02,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:02,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:02,790] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:02,791] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:02,791] [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
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	78.1576	307	1089	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.9783	315	1089	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.9239	306	1089	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	77.9234	318	1089	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	77.8688	352	1089	95	below_threshold
Pseudactinotalea terrae	strain=KACC 16542	GCA_009733845.1	1743262	1743262	type	True	77.8661	308	1089	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	77.8527	333	1089	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.8207	335	1089	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	77.807	354	1089	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	77.7684	305	1089	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	77.7623	313	1089	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	77.67	273	1089	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	77.6075	316	1089	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	77.5659	321	1089	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	77.5529	342	1089	95	below_threshold
Ruania rhizosphaerae	strain=LNNU 22110	GCA_009805705.1	1840413	1840413	type	True	77.5378	278	1089	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	77.5051	291	1089	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.4383	294	1089	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	77.438	304	1089	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.4281	331	1089	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.4212	317	1089	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	77.3967	273	1089	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	77.3643	285	1089	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	77.3612	287	1089	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.3446	296	1089	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.2166	309	1089	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.8981	198	1089	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	76.3108	232	1089	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	76.2171	255	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:02,793] [INFO] DFAST Taxonomy check result was written to GCF_002563925.1_ASM256392v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:02,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:02,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:02,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference/checkm_data
[2024-01-24 11:27:02,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:02,834] [INFO] Task started: CheckM
[2024-01-24 11:27:02,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563925.1_ASM256392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563925.1_ASM256392v1_genomic.fna/checkm_input GCF_002563925.1_ASM256392v1_genomic.fna/checkm_result
[2024-01-24 11:28:10,265] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:10,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:10,287] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:10,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:10,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563925.1_ASM256392v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:10,288] [INFO] Task started: Blastn
[2024-01-24 11:28:10,288] [INFO] Running command: blastn -query GCF_002563925.1_ASM256392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff91f9e8-758e-47e8-97e5-690bb4c8161e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563925.1_ASM256392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:12,040] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:12,048] [INFO] Selected 17 target genomes.
[2024-01-24 11:28:12,048] [INFO] Target genome list was writen to GCF_002563925.1_ASM256392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:12,061] [INFO] Task started: fastANI
[2024-01-24 11:28:12,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg0edd6e16-cfd9-4bdd-9c7f-5a344db9364c/GCF_002563925.1_ASM256392v1_genomic.fna.gz --refList GCF_002563925.1_ASM256392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563925.1_ASM256392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:24,158] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:24,183] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:24,183] [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_002563925.1	s__Serinibacter salmoneus	100.0	1083	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003121705.1	s__Serinibacter_A sp003121705	79.5211	487	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006351005.1	s__Miniimonas arenae	79.0339	467	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	-
GCF_004786095.1	s__Serinibacter_A arcticus	79.0197	469	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751805.1	s__Salana multivorans	78.5762	408	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	-
GCF_000421225.1	s__Ruania albidiflava	78.1465	308	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	78.0829	318	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352065.1	s__Georgenia sp006352065	77.9922	305	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_013085345.1	s__Isoptericola sediminis	77.8041	290	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116305.1	s__Ruania gallistercoris	77.7927	256	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900046455.1	s__Cellulomonas timonensis	77.7491	308	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000023105.1	s__Beutenbergia cavernae	77.586	338	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Beutenbergia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565425.1	s__Actinotalea sp017565425	77.5681	285	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	77.4659	326	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_901521055.1	s__Cellulomonas hominis_C	77.4598	347	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900163555.1	s__JB111 sp900163555	77.4084	220	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__JB111	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	77.3618	310	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:24,185] [INFO] GTDB search result was written to GCF_002563925.1_ASM256392v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:24,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:24,190] [INFO] DFAST_QC result json was written to GCF_002563925.1_ASM256392v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:24,191] [INFO] DFAST_QC completed!
[2024-01-24 11:28:24,191] [INFO] Total running time: 0h1m56s