[2023-06-29 16:38:43,239] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:38:43,241] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:38:43,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference
[2023-06-29 16:38:44,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:38:44,427] [INFO] Task started: Prodigal
[2023-06-29 16:38:44,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg7af4204a-0c62-4142-9dfe-b7363abdf963/GCA_021792455.1_ASM2179245v1_genomic.fna.gz | prodigal -d GCA_021792455.1_ASM2179245v1_genomic.fna/cds.fna -a GCA_021792455.1_ASM2179245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:38:52,062] [INFO] Task succeeded: Prodigal
[2023-06-29 16:38:52,062] [INFO] Task started: HMMsearch
[2023-06-29 16:38:52,062] [INFO] Running command: hmmsearch --tblout GCA_021792455.1_ASM2179245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference/reference_markers.hmm GCA_021792455.1_ASM2179245v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:38:52,281] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:38:52,283] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7af4204a-0c62-4142-9dfe-b7363abdf963/GCA_021792455.1_ASM2179245v1_genomic.fna.gz]
[2023-06-29 16:38:52,315] [INFO] Query marker FASTA was written to GCA_021792455.1_ASM2179245v1_genomic.fna/markers.fasta
[2023-06-29 16:38:52,315] [INFO] Task started: Blastn
[2023-06-29 16:38:52,315] [INFO] Running command: blastn -query GCA_021792455.1_ASM2179245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference/reference_markers.fasta -out GCA_021792455.1_ASM2179245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:38:52,916] [INFO] Task succeeded: Blastn
[2023-06-29 16:38:52,921] [INFO] Selected 12 target genomes.
[2023-06-29 16:38:52,922] [INFO] Target genome list was writen to GCA_021792455.1_ASM2179245v1_genomic.fna/target_genomes.txt
[2023-06-29 16:38:52,927] [INFO] Task started: fastANI
[2023-06-29 16:38:52,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg7af4204a-0c62-4142-9dfe-b7363abdf963/GCA_021792455.1_ASM2179245v1_genomic.fna.gz --refList GCA_021792455.1_ASM2179245v1_genomic.fna/target_genomes.txt --output GCA_021792455.1_ASM2179245v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:39:00,813] [INFO] Task succeeded: fastANI
[2023-06-29 16:39:00,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:39:00,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:39:00,826] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:39:00,826] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:39:00,826] [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
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.84	231	934	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	76.7773	220	934	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	76.7717	234	934	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	76.4491	191	934	95	below_threshold
Thermoleophilum album	strain=ATCC 35263	GCA_900108055.1	29539	29539	type	True	76.3934	79	934	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	76.0802	154	934	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	75.9577	101	934	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	75.109	70	934	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:39:00,828] [INFO] DFAST Taxonomy check result was written to GCA_021792455.1_ASM2179245v1_genomic.fna/tc_result.tsv
[2023-06-29 16:39:00,828] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:39:00,829] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:39:00,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference/checkm_data
[2023-06-29 16:39:00,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:39:00,861] [INFO] Task started: CheckM
[2023-06-29 16:39:00,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021792455.1_ASM2179245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021792455.1_ASM2179245v1_genomic.fna/checkm_input GCA_021792455.1_ASM2179245v1_genomic.fna/checkm_result
[2023-06-29 16:39:40,623] [INFO] Task succeeded: CheckM
[2023-06-29 16:39:40,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:39:40,647] [INFO] ===== Completeness check finished =====
[2023-06-29 16:39:40,648] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:39:40,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021792455.1_ASM2179245v1_genomic.fna/markers.fasta)
[2023-06-29 16:39:40,648] [INFO] Task started: Blastn
[2023-06-29 16:39:40,649] [INFO] Running command: blastn -query GCA_021792455.1_ASM2179245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a44e3da-5fe0-4ee9-ba8c-dc635db9d121/dqc_reference/reference_markers_gtdb.fasta -out GCA_021792455.1_ASM2179245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:39:41,444] [INFO] Task succeeded: Blastn
[2023-06-29 16:39:41,449] [INFO] Selected 16 target genomes.
[2023-06-29 16:39:41,449] [INFO] Target genome list was writen to GCA_021792455.1_ASM2179245v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:39:41,458] [INFO] Task started: fastANI
[2023-06-29 16:39:41,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg7af4204a-0c62-4142-9dfe-b7363abdf963/GCA_021792455.1_ASM2179245v1_genomic.fna.gz --refList GCA_021792455.1_ASM2179245v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021792455.1_ASM2179245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:39:51,136] [INFO] Task succeeded: fastANI
[2023-06-29 16:39:51,151] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:39:51,151] [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_017882445.1	s__Palsa-744 sp017882445	77.8719	196	934	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_013815355.1	s__Palsa-744 sp013815355	77.5903	211	934	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	77.4796	218	934	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_003134675.1	s__Palsa-744 sp003134675	77.3691	104	934	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_009781575.1	s__Palsa-744 sp009781575	77.3498	123	934	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	77.3166	195	934	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_003138355.1	s__Palsa-513 sp003138355	76.9743	139	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-513	95.0	99.90	99.88	0.98	0.98	4	-
GCA_018268595.1	s__Conexibacter sp018268595	76.9493	226	934	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	76.6466	187	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133565.1	s__Palsa-513 sp003133565	76.6419	110	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-513	95.0	99.70	99.65	0.91	0.91	3	-
GCA_005883215.1	s__AC-64 sp005883215	76.6215	120	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__AC-64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151895.1	s__Palsa-744 sp003151895	76.5026	148	934	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_016463765.1	s__SYBY01 sp016463765	76.4458	157	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424625.1	s__Baekduia woesei_A	76.4454	191	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003244205.1	s__QHBW01 sp003244205	76.3679	112	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__QHBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788585.1	s__SYBY01 sp005788585	75.8254	94	934	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:39:51,153] [INFO] GTDB search result was written to GCA_021792455.1_ASM2179245v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:39:51,154] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:39:51,158] [INFO] DFAST_QC result json was written to GCA_021792455.1_ASM2179245v1_genomic.fna/dqc_result.json
[2023-06-29 16:39:51,158] [INFO] DFAST_QC completed!
[2023-06-29 16:39:51,158] [INFO] Total running time: 0h1m8s