[2023-06-30 07:42:21,625] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:42:21,631] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:42:21,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference
[2023-06-30 07:42:22,958] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:42:22,959] [INFO] Task started: Prodigal
[2023-06-30 07:42:22,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg0aa708db-eb3b-495c-99ba-c4b6e8b96872/GCA_025355255.1_ASM2535525v1_genomic.fna.gz | prodigal -d GCA_025355255.1_ASM2535525v1_genomic.fna/cds.fna -a GCA_025355255.1_ASM2535525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:42:29,954] [INFO] Task succeeded: Prodigal
[2023-06-30 07:42:29,954] [INFO] Task started: HMMsearch
[2023-06-30 07:42:29,954] [INFO] Running command: hmmsearch --tblout GCA_025355255.1_ASM2535525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference/reference_markers.hmm GCA_025355255.1_ASM2535525v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:42:30,200] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:42:30,202] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0aa708db-eb3b-495c-99ba-c4b6e8b96872/GCA_025355255.1_ASM2535525v1_genomic.fna.gz]
[2023-06-30 07:42:30,237] [INFO] Query marker FASTA was written to GCA_025355255.1_ASM2535525v1_genomic.fna/markers.fasta
[2023-06-30 07:42:30,237] [INFO] Task started: Blastn
[2023-06-30 07:42:30,238] [INFO] Running command: blastn -query GCA_025355255.1_ASM2535525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference/reference_markers.fasta -out GCA_025355255.1_ASM2535525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:42:30,909] [INFO] Task succeeded: Blastn
[2023-06-30 07:42:30,913] [INFO] Selected 15 target genomes.
[2023-06-30 07:42:30,914] [INFO] Target genome list was writen to GCA_025355255.1_ASM2535525v1_genomic.fna/target_genomes.txt
[2023-06-30 07:42:30,915] [INFO] Task started: fastANI
[2023-06-30 07:42:30,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa708db-eb3b-495c-99ba-c4b6e8b96872/GCA_025355255.1_ASM2535525v1_genomic.fna.gz --refList GCA_025355255.1_ASM2535525v1_genomic.fna/target_genomes.txt --output GCA_025355255.1_ASM2535525v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:42:41,400] [INFO] Task succeeded: fastANI
[2023-06-30 07:42:41,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:42:41,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:42:41,406] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:42:41,407] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:42:41,407] [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
Actinomadura rudentiformis	strain=HMC1	GCA_008923185.1	359158	359158	type	True	74.8963	65	639	95	below_threshold
Actinomadura algeriensis	strain=DSM 46744	GCA_014873935.1	1679523	1679523	type	True	74.8919	75	639	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	74.7469	53	639	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.6572	51	639	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:42:41,409] [INFO] DFAST Taxonomy check result was written to GCA_025355255.1_ASM2535525v1_genomic.fna/tc_result.tsv
[2023-06-30 07:42:41,410] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:42:41,410] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:42:41,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference/checkm_data
[2023-06-30 07:42:41,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:42:41,450] [INFO] Task started: CheckM
[2023-06-30 07:42:41,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025355255.1_ASM2535525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025355255.1_ASM2535525v1_genomic.fna/checkm_input GCA_025355255.1_ASM2535525v1_genomic.fna/checkm_result
[2023-06-30 07:43:07,496] [INFO] Task succeeded: CheckM
[2023-06-30 07:43:07,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 07:43:07,518] [INFO] ===== Completeness check finished =====
[2023-06-30 07:43:07,518] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:43:07,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025355255.1_ASM2535525v1_genomic.fna/markers.fasta)
[2023-06-30 07:43:07,519] [INFO] Task started: Blastn
[2023-06-30 07:43:07,519] [INFO] Running command: blastn -query GCA_025355255.1_ASM2535525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcbfd41d-84b9-40ea-a083-8a05be2dd46d/dqc_reference/reference_markers_gtdb.fasta -out GCA_025355255.1_ASM2535525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:43:08,533] [INFO] Task succeeded: Blastn
[2023-06-30 07:43:08,538] [INFO] Selected 18 target genomes.
[2023-06-30 07:43:08,538] [INFO] Target genome list was writen to GCA_025355255.1_ASM2535525v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:43:08,541] [INFO] Task started: fastANI
[2023-06-30 07:43:08,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aa708db-eb3b-495c-99ba-c4b6e8b96872/GCA_025355255.1_ASM2535525v1_genomic.fna.gz --refList GCA_025355255.1_ASM2535525v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025355255.1_ASM2535525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:43:16,812] [INFO] Task succeeded: fastANI
[2023-06-30 07:43:16,828] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 07:43:16,828] [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_903925955.1	s__CAIXZV01 sp903925955	83.7952	446	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIXZV01	95.0	98.48	97.83	0.88	0.83	4	-
GCA_903924005.1	s__CAIXZV01 sp903924005	83.6312	412	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIXZV01	95.0	99.66	99.58	0.88	0.87	3	-
GCA_903930745.1	s__CAIXZV01 sp903930745	78.7049	217	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIXZV01	95.0	99.19	99.11	0.83	0.82	3	-
GCA_001443375.1	s__CSP1-4 sp001443375	77.3048	117	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CSP1-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822495.1	s__CAIJPD01 sp903822495	77.2443	146	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIJPD01	95.0	99.94	99.94	0.97	0.97	2	-
GCA_016191345.1	s__UBA5189 sp016191345	77.061	128	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250155.1	s__UBA5189 sp003250155	77.0033	83	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	99.47	99.47	0.88	0.88	2	-
GCA_002413045.1	s__UBA5189 sp002413045	76.8981	100	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889475.1	s__UBA5189 sp005889475	76.8965	97	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200675.1	s__UBA5189 sp016200675	76.8922	102	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478725.1	s__C-114 sp015478725	76.8112	106	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698385.1	s__SPCO01 sp013698385	76.7693	52	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__SPCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882635.1	s__CF-46 sp005882635	76.7175	111	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003171035.1	s__Fen-1039 sp003171035	76.6751	68	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881905.1	s__Chersky-267 sp017881905	76.651	92	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Chersky-267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141955.1	s__Fen-1039 sp003141955	76.5755	84	639	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.62	99.62	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-30 07:43:16,830] [INFO] GTDB search result was written to GCA_025355255.1_ASM2535525v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:43:16,831] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:43:16,834] [INFO] DFAST_QC result json was written to GCA_025355255.1_ASM2535525v1_genomic.fna/dqc_result.json
[2023-06-30 07:43:16,834] [INFO] DFAST_QC completed!
[2023-06-30 07:43:16,834] [INFO] Total running time: 0h0m55s