[2023-06-28 23:25:44,839] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:25:44,847] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:25:44,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference
[2023-06-28 23:25:46,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:25:46,690] [INFO] Task started: Prodigal
[2023-06-28 23:25:46,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b8ce295-5ffb-4c0a-829b-8d990044efc8/GCA_017304895.1_ASM1730489v1_genomic.fna.gz | prodigal -d GCA_017304895.1_ASM1730489v1_genomic.fna/cds.fna -a GCA_017304895.1_ASM1730489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:25:52,761] [INFO] Task succeeded: Prodigal
[2023-06-28 23:25:52,761] [INFO] Task started: HMMsearch
[2023-06-28 23:25:52,761] [INFO] Running command: hmmsearch --tblout GCA_017304895.1_ASM1730489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference/reference_markers.hmm GCA_017304895.1_ASM1730489v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:25:52,994] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:25:52,995] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b8ce295-5ffb-4c0a-829b-8d990044efc8/GCA_017304895.1_ASM1730489v1_genomic.fna.gz]
[2023-06-28 23:25:53,027] [INFO] Query marker FASTA was written to GCA_017304895.1_ASM1730489v1_genomic.fna/markers.fasta
[2023-06-28 23:25:53,028] [INFO] Task started: Blastn
[2023-06-28 23:25:53,028] [INFO] Running command: blastn -query GCA_017304895.1_ASM1730489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference/reference_markers.fasta -out GCA_017304895.1_ASM1730489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:54,212] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:54,215] [INFO] Selected 30 target genomes.
[2023-06-28 23:25:54,215] [INFO] Target genome list was writen to GCA_017304895.1_ASM1730489v1_genomic.fna/target_genomes.txt
[2023-06-28 23:25:54,220] [INFO] Task started: fastANI
[2023-06-28 23:25:54,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8ce295-5ffb-4c0a-829b-8d990044efc8/GCA_017304895.1_ASM1730489v1_genomic.fna.gz --refList GCA_017304895.1_ASM1730489v1_genomic.fna/target_genomes.txt --output GCA_017304895.1_ASM1730489v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:26:14,239] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:14,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:26:14,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:26:14,256] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:26:14,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:26:14,257] [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 hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.0451	261	641	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.0252	258	641	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	77.8531	211	641	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	77.8467	282	641	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.8313	249	641	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.7661	250	641	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	77.7158	225	641	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	77.7023	222	641	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	77.6944	243	641	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.693	242	641	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.6748	223	641	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.6626	269	641	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	77.6554	238	641	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.604	264	641	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	77.5893	268	641	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	77.5553	234	641	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.545	278	641	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	77.5117	240	641	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	77.4717	231	641	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	77.4622	231	641	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	77.4175	253	641	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	77.367	221	641	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	77.3177	159	641	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	77.2875	234	641	95	below_threshold
Brevibacterium casei	strain=CIP 102111	GCA_900169275.1	33889	33889	type	True	76.7042	109	641	95	below_threshold
Brevibacterium casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	76.6855	111	641	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	76.5866	121	641	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	76.4529	169	641	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	76.4352	167	641	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	75.8471	149	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:26:14,259] [INFO] DFAST Taxonomy check result was written to GCA_017304895.1_ASM1730489v1_genomic.fna/tc_result.tsv
[2023-06-28 23:26:14,259] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:26:14,259] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:26:14,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference/checkm_data
[2023-06-28 23:26:14,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:26:14,297] [INFO] Task started: CheckM
[2023-06-28 23:26:14,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017304895.1_ASM1730489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017304895.1_ASM1730489v1_genomic.fna/checkm_input GCA_017304895.1_ASM1730489v1_genomic.fna/checkm_result
[2023-06-28 23:26:35,631] [INFO] Task succeeded: CheckM
[2023-06-28 23:26:35,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:26:35,649] [INFO] ===== Completeness check finished =====
[2023-06-28 23:26:35,650] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:26:35,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017304895.1_ASM1730489v1_genomic.fna/markers.fasta)
[2023-06-28 23:26:35,650] [INFO] Task started: Blastn
[2023-06-28 23:26:35,650] [INFO] Running command: blastn -query GCA_017304895.1_ASM1730489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3caa2763-89da-4057-bbce-026c807110ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_017304895.1_ASM1730489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:26:37,641] [INFO] Task succeeded: Blastn
[2023-06-28 23:26:37,644] [INFO] Selected 17 target genomes.
[2023-06-28 23:26:37,645] [INFO] Target genome list was writen to GCA_017304895.1_ASM1730489v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:26:37,708] [INFO] Task started: fastANI
[2023-06-28 23:26:37,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8ce295-5ffb-4c0a-829b-8d990044efc8/GCA_017304895.1_ASM1730489v1_genomic.fna.gz --refList GCA_017304895.1_ASM1730489v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017304895.1_ASM1730489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:26:49,757] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:49,768] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:26:49,768] [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_003751805.1	s__Salana multivorans	98.7184	585	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	conclusive
GCF_006351005.1	s__Miniimonas arenae	80.642	330	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	-
GCF_003121705.1	s__Serinibacter_A sp003121705	79.6683	336	641	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_004786095.1	s__Serinibacter_A arcticus	79.6072	307	641	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_002563925.1	s__Serinibacter salmoneus	78.3506	201	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	77.9485	244	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	77.8586	256	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_016907365.1	s__Oerskovia paurometabola	77.6434	230	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.20	99.20	0.97	0.97	2	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	77.6393	256	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	77.5241	239	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	77.4956	285	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_018388465.1	s__Cellulomonas sp018388465	77.4415	223	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_900169275.1	s__Brevibacterium casei	76.6653	111	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.23	97.33	0.93	0.90	17	-
GCF_000960475.2	s__Nocardioides luteus_A	76.143	152	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	76.1133	191	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	76.0509	199	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117935.1	s__Streptomyces roseicoloratus	76.0389	187	641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:26:49,770] [INFO] GTDB search result was written to GCA_017304895.1_ASM1730489v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:26:49,770] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:26:49,774] [INFO] DFAST_QC result json was written to GCA_017304895.1_ASM1730489v1_genomic.fna/dqc_result.json
[2023-06-28 23:26:49,774] [INFO] DFAST_QC completed!
[2023-06-28 23:26:49,774] [INFO] Total running time: 0h1m5s