[2023-06-29 16:09:02,221] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:09:02,224] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:09:02,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference
[2023-06-29 16:09:03,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:09:03,511] [INFO] Task started: Prodigal
[2023-06-29 16:09:03,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ba88a29-398f-41df-b596-e1d837c30356/GCA_021838405.1_ASM2183840v1_genomic.fna.gz | prodigal -d GCA_021838405.1_ASM2183840v1_genomic.fna/cds.fna -a GCA_021838405.1_ASM2183840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:09:07,911] [INFO] Task succeeded: Prodigal
[2023-06-29 16:09:07,911] [INFO] Task started: HMMsearch
[2023-06-29 16:09:07,912] [INFO] Running command: hmmsearch --tblout GCA_021838405.1_ASM2183840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference/reference_markers.hmm GCA_021838405.1_ASM2183840v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:09:08,130] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:09:08,132] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ba88a29-398f-41df-b596-e1d837c30356/GCA_021838405.1_ASM2183840v1_genomic.fna.gz]
[2023-06-29 16:09:08,154] [INFO] Query marker FASTA was written to GCA_021838405.1_ASM2183840v1_genomic.fna/markers.fasta
[2023-06-29 16:09:08,154] [INFO] Task started: Blastn
[2023-06-29 16:09:08,154] [INFO] Running command: blastn -query GCA_021838405.1_ASM2183840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference/reference_markers.fasta -out GCA_021838405.1_ASM2183840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:08,817] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:08,821] [INFO] Selected 29 target genomes.
[2023-06-29 16:09:08,821] [INFO] Target genome list was writen to GCA_021838405.1_ASM2183840v1_genomic.fna/target_genomes.txt
[2023-06-29 16:09:08,824] [INFO] Task started: fastANI
[2023-06-29 16:09:08,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ba88a29-398f-41df-b596-e1d837c30356/GCA_021838405.1_ASM2183840v1_genomic.fna.gz --refList GCA_021838405.1_ASM2183840v1_genomic.fna/target_genomes.txt --output GCA_021838405.1_ASM2183840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:09:30,365] [INFO] Task succeeded: fastANI
[2023-06-29 16:09:30,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:09:30,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:09:30,374] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:09:30,375] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:09:30,375] [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
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	75.0808	55	493	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	74.9779	53	493	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	74.9408	57	493	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:09:30,378] [INFO] DFAST Taxonomy check result was written to GCA_021838405.1_ASM2183840v1_genomic.fna/tc_result.tsv
[2023-06-29 16:09:30,378] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:09:30,379] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:09:30,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference/checkm_data
[2023-06-29 16:09:30,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:09:30,401] [INFO] Task started: CheckM
[2023-06-29 16:09:30,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021838405.1_ASM2183840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021838405.1_ASM2183840v1_genomic.fna/checkm_input GCA_021838405.1_ASM2183840v1_genomic.fna/checkm_result
[2023-06-29 16:09:49,770] [INFO] Task succeeded: CheckM
[2023-06-29 16:09:49,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:09:49,791] [INFO] ===== Completeness check finished =====
[2023-06-29 16:09:49,791] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:09:49,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021838405.1_ASM2183840v1_genomic.fna/markers.fasta)
[2023-06-29 16:09:49,792] [INFO] Task started: Blastn
[2023-06-29 16:09:49,792] [INFO] Running command: blastn -query GCA_021838405.1_ASM2183840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96c81b2a-f0e8-4d59-a6ce-4b6282014044/dqc_reference/reference_markers_gtdb.fasta -out GCA_021838405.1_ASM2183840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:50,756] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:50,761] [INFO] Selected 19 target genomes.
[2023-06-29 16:09:50,761] [INFO] Target genome list was writen to GCA_021838405.1_ASM2183840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:09:50,763] [INFO] Task started: fastANI
[2023-06-29 16:09:50,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ba88a29-398f-41df-b596-e1d837c30356/GCA_021838405.1_ASM2183840v1_genomic.fna.gz --refList GCA_021838405.1_ASM2183840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021838405.1_ASM2183840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:09:57,933] [INFO] Task succeeded: fastANI
[2023-06-29 16:09:57,955] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:09:57,955] [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_001443545.1	s__RAAP-2 sp001443545	81.1747	253	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971185.1	s__RAAP-2 sp018971185	78.5964	128	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138815.1	s__RAAP-2 sp003138815	78.4065	156	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.69	0.94	0.86	28	-
GCA_017883045.1	s__RAAP-2 sp017883045	78.3112	150	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903860745.1	s__RAAP-2 sp903860745	78.2074	125	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.88	99.81	0.92	0.91	5	-
GCA_002255565.1	s__RAAP-2 sp002255565	78.019	127	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158855.1	s__RAAP-2 sp003158855	77.9616	130	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133665.1	s__RAAP-2 sp003133665	77.7407	141	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167415.1	s__RAAP-2 sp003167415	77.4804	102	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	96.12	96.12	0.82	0.82	2	-
GCA_003132205.1	s__RAAP-2 sp003132205	77.432	142	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155915.1	s__RAAP-2 sp003155915	77.4303	111	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.91	99.78	0.97	0.95	27	-
GCA_017882985.1	s__RAAP-2 sp017882985	77.337	72	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133685.1	s__RAAP-2 sp003133685	77.2453	102	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	98.41	97.01	0.93	0.87	3	-
GCA_003151555.1	s__RAAP-2 sp003151555	77.1559	72	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136415.1	s__RAAP-2 sp003136415	77.1543	90	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003131665.1	s__RAAP-2 sp003131665	76.946	75	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162475.1	s__RAAP-2 sp003162475	76.8813	104	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141815.1	s__RAAP-2 sp003141815	76.7051	101	493	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:09:57,957] [INFO] GTDB search result was written to GCA_021838405.1_ASM2183840v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:09:57,958] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:09:57,961] [INFO] DFAST_QC result json was written to GCA_021838405.1_ASM2183840v1_genomic.fna/dqc_result.json
[2023-06-29 16:09:57,961] [INFO] DFAST_QC completed!
[2023-06-29 16:09:57,962] [INFO] Total running time: 0h0m56s