[2023-06-28 14:20:25,226] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:20:25,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:20:25,229] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference
[2023-06-28 14:20:26,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:20:26,448] [INFO] Task started: Prodigal
[2023-06-28 14:20:26,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg52695729-2698-4305-af61-a079f008f5ef/GCA_005883215.1_ASM588321v1_genomic.fna.gz | prodigal -d GCA_005883215.1_ASM588321v1_genomic.fna/cds.fna -a GCA_005883215.1_ASM588321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:20:43,787] [INFO] Task succeeded: Prodigal
[2023-06-28 14:20:43,788] [INFO] Task started: HMMsearch
[2023-06-28 14:20:43,788] [INFO] Running command: hmmsearch --tblout GCA_005883215.1_ASM588321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference/reference_markers.hmm GCA_005883215.1_ASM588321v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:20:43,978] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:20:43,979] [INFO] Found 6/6 markers.
[2023-06-28 14:20:44,016] [INFO] Query marker FASTA was written to GCA_005883215.1_ASM588321v1_genomic.fna/markers.fasta
[2023-06-28 14:20:44,016] [INFO] Task started: Blastn
[2023-06-28 14:20:44,016] [INFO] Running command: blastn -query GCA_005883215.1_ASM588321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference/reference_markers.fasta -out GCA_005883215.1_ASM588321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:20:44,666] [INFO] Task succeeded: Blastn
[2023-06-28 14:20:44,670] [INFO] Selected 13 target genomes.
[2023-06-28 14:20:44,671] [INFO] Target genome list was writen to GCA_005883215.1_ASM588321v1_genomic.fna/target_genomes.txt
[2023-06-28 14:20:44,671] [INFO] Task started: fastANI
[2023-06-28 14:20:44,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg52695729-2698-4305-af61-a079f008f5ef/GCA_005883215.1_ASM588321v1_genomic.fna.gz --refList GCA_005883215.1_ASM588321v1_genomic.fna/target_genomes.txt --output GCA_005883215.1_ASM588321v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:20:56,016] [INFO] Task succeeded: fastANI
[2023-06-28 14:20:56,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:20:56,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:20:56,027] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:20:56,027] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:20:56,027] [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
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	77.4233	389	1068	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.3873	395	1068	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.3118	371	1068	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	77.1018	330	1068	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.9424	360	1068	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	76.5928	335	1068	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	76.5278	291	1068	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.1391	230	1068	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	74.9907	132	1068	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	74.9434	164	1068	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	74.9212	98	1068	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:20:56,030] [INFO] DFAST Taxonomy check result was written to GCA_005883215.1_ASM588321v1_genomic.fna/tc_result.tsv
[2023-06-28 14:20:56,032] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:20:56,032] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:20:56,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference/checkm_data
[2023-06-28 14:20:56,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:20:56,067] [INFO] Task started: CheckM
[2023-06-28 14:20:56,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005883215.1_ASM588321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005883215.1_ASM588321v1_genomic.fna/checkm_input GCA_005883215.1_ASM588321v1_genomic.fna/checkm_result
[2023-06-28 14:21:42,545] [INFO] Task succeeded: CheckM
[2023-06-28 14:21:42,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:21:42,569] [INFO] ===== Completeness check finished =====
[2023-06-28 14:21:42,570] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:21:42,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005883215.1_ASM588321v1_genomic.fna/markers.fasta)
[2023-06-28 14:21:42,570] [INFO] Task started: Blastn
[2023-06-28 14:21:42,570] [INFO] Running command: blastn -query GCA_005883215.1_ASM588321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a30de8f-a5b4-4c8c-8a2a-5e244482c267/dqc_reference/reference_markers_gtdb.fasta -out GCA_005883215.1_ASM588321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:21:43,546] [INFO] Task succeeded: Blastn
[2023-06-28 14:21:43,549] [INFO] Selected 19 target genomes.
[2023-06-28 14:21:43,550] [INFO] Target genome list was writen to GCA_005883215.1_ASM588321v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:21:43,554] [INFO] Task started: fastANI
[2023-06-28 14:21:43,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg52695729-2698-4305-af61-a079f008f5ef/GCA_005883215.1_ASM588321v1_genomic.fna.gz --refList GCA_005883215.1_ASM588321v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005883215.1_ASM588321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:21:55,281] [INFO] Task succeeded: fastANI
[2023-06-28 14:21:55,298] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:21:55,298] [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_005883215.1	s__AC-64 sp005883215	100.0	1066	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__AC-64	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005883255.1	s__AC-38 sp005883255	78.7231	259	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__AC-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813955.1	s__CADCVQ01 sp013813955	78.35	222	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815355.1	s__Palsa-744 sp013815355	78.2942	251	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882445.1	s__Palsa-744 sp017882445	78.16	276	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882375.1	s__Palsa-744 sp017882375	78.0987	319	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882455.1	s__Palsa-744 sp017882455	78.0323	313	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884115.1	s__Palsa-744 sp005884115	77.841	284	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882465.1	s__Palsa-465 sp017882465	77.6371	280	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830015.1	s__F1-60-MAGs163 sp903830015	77.4797	134	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	96.97	95.76	0.83	0.75	5	-
GCA_018268595.1	s__Conexibacter sp018268595	77.4239	328	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	77.4219	324	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	77.3559	354	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240015.1	s__Palsa-465 sp019240015	77.251	193	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132505.1	s__Palsa-513 sp003132505	77.2326	192	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-513	95.0	99.81	99.53	0.95	0.93	7	-
GCF_000025265.1	s__Conexibacter woesei	76.9196	364	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699915.1	s__F1-60-MAGs163 sp009699915	76.8471	99	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240225.1	s__Patulibacter medicamentivorans	76.5251	290	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Patulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788585.1	s__SYBY01 sp005788585	76.0338	209	1068	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:21:55,300] [INFO] GTDB search result was written to GCA_005883215.1_ASM588321v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:21:55,301] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:21:55,305] [INFO] DFAST_QC result json was written to GCA_005883215.1_ASM588321v1_genomic.fna/dqc_result.json
[2023-06-28 14:21:55,305] [INFO] DFAST_QC completed!
[2023-06-28 14:21:55,305] [INFO] Total running time: 0h1m30s