[2024-01-24 13:57:44,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference
[2024-01-24 13:57:45,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,894] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg1019f10b-97af-4efa-98f4-6caf9d93d638/GCF_014208035.1_ASM1420803v1_genomic.fna.gz | prodigal -d GCF_014208035.1_ASM1420803v1_genomic.fna/cds.fna -a GCF_014208035.1_ASM1420803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:53,350] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:53,350] [INFO] Task started: HMMsearch
[2024-01-24 13:57:53,350] [INFO] Running command: hmmsearch --tblout GCF_014208035.1_ASM1420803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference/reference_markers.hmm GCF_014208035.1_ASM1420803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:53,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:53,595] [INFO] Found 6/6 markers.
[2024-01-24 13:57:53,625] [INFO] Query marker FASTA was written to GCF_014208035.1_ASM1420803v1_genomic.fna/markers.fasta
[2024-01-24 13:57:53,626] [INFO] Task started: Blastn
[2024-01-24 13:57:53,626] [INFO] Running command: blastn -query GCF_014208035.1_ASM1420803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference/reference_markers.fasta -out GCF_014208035.1_ASM1420803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:54,773] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:54,778] [INFO] Selected 22 target genomes.
[2024-01-24 13:57:54,778] [INFO] Target genome list was writen to GCF_014208035.1_ASM1420803v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:54,804] [INFO] Task started: fastANI
[2024-01-24 13:57:54,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg1019f10b-97af-4efa-98f4-6caf9d93d638/GCF_014208035.1_ASM1420803v1_genomic.fna.gz --refList GCF_014208035.1_ASM1420803v1_genomic.fna/target_genomes.txt --output GCF_014208035.1_ASM1420803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:05,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:05,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:05,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:05,480] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:05,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:05,480] [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
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	100.0	874	882	95	conclusive
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	79.2825	250	882	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	78.9765	198	882	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	78.9493	269	882	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	78.9426	203	882	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	78.7666	250	882	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	78.7436	149	882	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	78.5399	207	882	95	below_threshold
Actinomyces howellii	strain=NCTC11636	GCA_900637165.1	52771	52771	type	True	78.4069	218	882	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	78.2231	213	882	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	78.1961	205	882	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	78.0782	198	882	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.0459	214	882	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	77.4755	172	882	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.2761	151	882	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	77.2526	135	882	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.2505	133	882	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	77.0902	160	882	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	76.9969	164	882	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	76.9956	165	882	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	76.883	125	882	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	76.3482	109	882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:05,482] [INFO] DFAST Taxonomy check result was written to GCF_014208035.1_ASM1420803v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:05,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:05,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:05,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference/checkm_data
[2024-01-24 13:58:05,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:05,512] [INFO] Task started: CheckM
[2024-01-24 13:58:05,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014208035.1_ASM1420803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014208035.1_ASM1420803v1_genomic.fna/checkm_input GCF_014208035.1_ASM1420803v1_genomic.fna/checkm_result
[2024-01-24 13:58:35,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:35,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,334] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:35,334] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:35,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014208035.1_ASM1420803v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:35,335] [INFO] Task started: Blastn
[2024-01-24 13:58:35,336] [INFO] Running command: blastn -query GCF_014208035.1_ASM1420803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65313fc4-c805-433a-a08f-79071a039d2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014208035.1_ASM1420803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,012] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,015] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:37,015] [INFO] Target genome list was writen to GCF_014208035.1_ASM1420803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:37,038] [INFO] Task started: fastANI
[2024-01-24 13:58:37,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg1019f10b-97af-4efa-98f4-6caf9d93d638/GCF_014208035.1_ASM1420803v1_genomic.fna.gz --refList GCF_014208035.1_ASM1420803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014208035.1_ASM1420803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:44,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:44,495] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:44,496] [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_014208035.1	s__Pauljensenia hyovaginalis	100.0	875	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	conclusive
GCF_900499005.1	s__Pauljensenia culturomici	83.4189	534	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405145.1	s__Pauljensenia cardiffensis	80.472	326	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.37	97.30	0.94	0.93	4	-
GCF_900155595.1	s__Pauljensenia mediterranea	80.1679	365	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001072465.1	s__Pauljensenia sp001072465	79.7459	277	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_001838165.1	s__Pauljensenia sp001838165	79.6783	267	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCA_018375675.1	s__Pauljensenia sp018375675	79.6404	264	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018382595.1	s__Pauljensenia sp018382595	79.592	255	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466265.1	s__Pauljensenia sp000466265	79.5579	262	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
GCF_001746855.1	s__Pauljensenia hongkongensis	79.529	258	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.51	97.69	0.81	0.72	5	-
GCF_018986735.1	s__Pauljensenia sp018986735	79.3573	284	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411415.1	s__Pauljensenia sp000411415	79.3194	279	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCF_000820725.1	s__Pauljensenia polynesiensis	79.2822	250	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000429245.1	s__Pauljensenia georgiae	79.1782	308	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.90	96.98	0.94	0.93	3	-
GCF_000185285.1	s__Pauljensenia sp000185285	79.0483	249	882	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.02	95.63	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:44,499] [INFO] GTDB search result was written to GCF_014208035.1_ASM1420803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:44,499] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:44,507] [INFO] DFAST_QC result json was written to GCF_014208035.1_ASM1420803v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:44,507] [INFO] DFAST_QC completed!
[2024-01-24 13:58:44,507] [INFO] Total running time: 0h0m60s