[2023-06-30 19:04:47,801] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:04:47,804] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:04:47,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference
[2023-06-30 19:04:49,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:04:49,114] [INFO] Task started: Prodigal
[2023-06-30 19:04:49,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg19b26780-9bea-47bc-8277-ff53fc2f4a1a/GCA_025930975.1_ASM2593097v1_genomic.fna.gz | prodigal -d GCA_025930975.1_ASM2593097v1_genomic.fna/cds.fna -a GCA_025930975.1_ASM2593097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:04:54,463] [INFO] Task succeeded: Prodigal
[2023-06-30 19:04:54,464] [INFO] Task started: HMMsearch
[2023-06-30 19:04:54,464] [INFO] Running command: hmmsearch --tblout GCA_025930975.1_ASM2593097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference/reference_markers.hmm GCA_025930975.1_ASM2593097v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:04:54,699] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:04:54,701] [INFO] Found 6/6 markers.
[2023-06-30 19:04:54,731] [INFO] Query marker FASTA was written to GCA_025930975.1_ASM2593097v1_genomic.fna/markers.fasta
[2023-06-30 19:04:54,731] [INFO] Task started: Blastn
[2023-06-30 19:04:54,731] [INFO] Running command: blastn -query GCA_025930975.1_ASM2593097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference/reference_markers.fasta -out GCA_025930975.1_ASM2593097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:04:55,443] [INFO] Task succeeded: Blastn
[2023-06-30 19:04:55,447] [INFO] Selected 20 target genomes.
[2023-06-30 19:04:55,447] [INFO] Target genome list was writen to GCA_025930975.1_ASM2593097v1_genomic.fna/target_genomes.txt
[2023-06-30 19:04:55,450] [INFO] Task started: fastANI
[2023-06-30 19:04:55,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b26780-9bea-47bc-8277-ff53fc2f4a1a/GCA_025930975.1_ASM2593097v1_genomic.fna.gz --refList GCA_025930975.1_ASM2593097v1_genomic.fna/target_genomes.txt --output GCA_025930975.1_ASM2593097v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:05:11,070] [INFO] Task succeeded: fastANI
[2023-06-30 19:05:11,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:05:11,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:05:11,089] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:05:11,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:05:11,089] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	77.3365	278	765	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.6371	230	765	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.5576	306	765	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.4143	288	765	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.3992	206	765	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.397	255	765	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	75.3097	101	765	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.2577	216	765	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	75.257	268	765	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.241	225	765	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	75.049	175	765	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	74.9372	92	765	95	below_threshold
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	74.9274	141	765	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	74.9041	94	765	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	74.856	94	765	95	below_threshold
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	74.8532	155	765	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	74.7672	196	765	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	74.63	67	765	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:05:11,092] [INFO] DFAST Taxonomy check result was written to GCA_025930975.1_ASM2593097v1_genomic.fna/tc_result.tsv
[2023-06-30 19:05:11,092] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:05:11,093] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:05:11,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference/checkm_data
[2023-06-30 19:05:11,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:05:11,129] [INFO] Task started: CheckM
[2023-06-30 19:05:11,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025930975.1_ASM2593097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025930975.1_ASM2593097v1_genomic.fna/checkm_input GCA_025930975.1_ASM2593097v1_genomic.fna/checkm_result
[2023-06-30 19:05:33,169] [INFO] Task succeeded: CheckM
[2023-06-30 19:05:33,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 19:05:33,229] [INFO] ===== Completeness check finished =====
[2023-06-30 19:05:33,229] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:05:33,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025930975.1_ASM2593097v1_genomic.fna/markers.fasta)
[2023-06-30 19:05:33,230] [INFO] Task started: Blastn
[2023-06-30 19:05:33,230] [INFO] Running command: blastn -query GCA_025930975.1_ASM2593097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc11c2e29-bcb1-46e7-9174-406799c96574/dqc_reference/reference_markers_gtdb.fasta -out GCA_025930975.1_ASM2593097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:05:34,371] [INFO] Task succeeded: Blastn
[2023-06-30 19:05:34,376] [INFO] Selected 21 target genomes.
[2023-06-30 19:05:34,377] [INFO] Target genome list was writen to GCA_025930975.1_ASM2593097v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:05:34,390] [INFO] Task started: fastANI
[2023-06-30 19:05:34,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b26780-9bea-47bc-8277-ff53fc2f4a1a/GCA_025930975.1_ASM2593097v1_genomic.fna.gz --refList GCA_025930975.1_ASM2593097v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025930975.1_ASM2593097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:05:43,917] [INFO] Task succeeded: fastANI
[2023-06-30 19:05:43,939] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 19:05:43,939] [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
GCA_013697275.1	s__JACVSB01 sp013697275	78.2868	263	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVSB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696595.1	s__JACCYG01 sp013696595	78.1728	179	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534155.1	s__JACVSB01 sp014534155	78.0652	234	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVSB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134505.1	s__PALSA-612 sp003134505	77.9294	239	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__PALSA-612	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883335.1	s__AC-32 sp005883335	77.8153	225	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885565.1	s__AC-50 sp005885565	77.8066	299	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883235.1	s__AC-50 sp005883235	77.7976	169	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883965.1	s__AC-32 sp005883965	77.7924	227	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884575.1	s__AC-16 sp005884575	77.6234	312	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696185.1	s__JACCZA01 sp013696185	77.6131	215	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCZA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812235.1	s__JACCTU01 sp013812235	77.585	171	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695385.1	s__JACDAN01 sp013695385	77.543	182	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACDAN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236545.1	s__Palsa-739 sp019236545	77.5052	242	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	-
GCA_001920085.1	s__3-1-20CM-4-69-9 sp001920085	77.4589	163	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884155.1	s__AC-32 sp005884155	77.4417	210	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366385.1	s__GMQP-bins7 sp004366385	77.4386	304	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__GMQP-bins7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351045.1	s__Gaiella occulta	77.4241	270	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139545.1	s__Palsa-739 sp003139545	77.1532	255	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930195.1	s__PALSA-600 sp903930195	77.0099	162	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__PALSA-600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534345.1	s__JACVRR01 sp014534345	76.826	225	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132665.1	s__Fen-549 sp003132665	76.7084	118	765	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Fen-549	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:05:43,941] [INFO] GTDB search result was written to GCA_025930975.1_ASM2593097v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:05:43,942] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:05:43,947] [INFO] DFAST_QC result json was written to GCA_025930975.1_ASM2593097v1_genomic.fna/dqc_result.json
[2023-06-30 19:05:43,947] [INFO] DFAST_QC completed!
[2023-06-30 19:05:43,947] [INFO] Total running time: 0h0m56s