[2024-01-25 18:25:05,750] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:05,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:05,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference
[2024-01-25 18:25:06,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:06,951] [INFO] Task started: Prodigal
[2024-01-25 18:25:06,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c368bd2-d6d7-407d-a058-796a7791e0b3/GCF_001544975.2_ASM154497v2_genomic.fna.gz | prodigal -d GCF_001544975.2_ASM154497v2_genomic.fna/cds.fna -a GCF_001544975.2_ASM154497v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:30,338] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:30,339] [INFO] Task started: HMMsearch
[2024-01-25 18:25:30,339] [INFO] Running command: hmmsearch --tblout GCF_001544975.2_ASM154497v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference/reference_markers.hmm GCF_001544975.2_ASM154497v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:30,661] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:30,665] [INFO] Found 6/6 markers.
[2024-01-25 18:25:30,730] [INFO] Query marker FASTA was written to GCF_001544975.2_ASM154497v2_genomic.fna/markers.fasta
[2024-01-25 18:25:30,731] [INFO] Task started: Blastn
[2024-01-25 18:25:30,731] [INFO] Running command: blastn -query GCF_001544975.2_ASM154497v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference/reference_markers.fasta -out GCF_001544975.2_ASM154497v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:31,575] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:31,577] [INFO] Selected 12 target genomes.
[2024-01-25 18:25:31,577] [INFO] Target genome list was writen to GCF_001544975.2_ASM154497v2_genomic.fna/target_genomes.txt
[2024-01-25 18:25:31,582] [INFO] Task started: fastANI
[2024-01-25 18:25:31,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c368bd2-d6d7-407d-a058-796a7791e0b3/GCF_001544975.2_ASM154497v2_genomic.fna.gz --refList GCF_001544975.2_ASM154497v2_genomic.fna/target_genomes.txt --output GCF_001544975.2_ASM154497v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:55,491] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:55,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:55,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:55,500] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:25:55,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:55,500] [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
Caballeronia arationis		GCA_001544975.2	1777142	1777142	type	True	100.0	2827	2841	95	conclusive
Caballeronia telluris		GCA_001544495.2	326475	326475	type	True	92.3289	1833	2841	95	below_threshold
Caballeronia terrestris		GCA_001544515.2	1226301	1226301	type	True	87.1042	1784	2841	95	below_threshold
Caballeronia choica		GCA_001544535.2	326476	326476	type	True	86.8562	1724	2841	95	below_threshold
Caballeronia humi		GCA_001544475.2	326474	326474	type	True	86.6362	1753	2841	95	below_threshold
Caballeronia glathei	strain=LMG 14190	GCA_000751215.2	60547	60547	type	True	85.8519	1552	2841	95	below_threshold
Caballeronia glathei	strain=DSM 50014	GCA_000698595.1	60547	60547	type	True	85.8125	1581	2841	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	81.5661	1005	2841	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	81.3037	1289	2841	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	81.2287	1189	2841	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	81.2111	1020	2841	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	80.7121	1081	2841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:55,502] [INFO] DFAST Taxonomy check result was written to GCF_001544975.2_ASM154497v2_genomic.fna/tc_result.tsv
[2024-01-25 18:25:55,503] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:55,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:55,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference/checkm_data
[2024-01-25 18:25:55,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:55,589] [INFO] Task started: CheckM
[2024-01-25 18:25:55,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001544975.2_ASM154497v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001544975.2_ASM154497v2_genomic.fna/checkm_input GCF_001544975.2_ASM154497v2_genomic.fna/checkm_result
[2024-01-25 18:27:01,882] [INFO] Task succeeded: CheckM
[2024-01-25 18:27:01,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:27:01,909] [INFO] ===== Completeness check finished =====
[2024-01-25 18:27:01,909] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:27:01,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001544975.2_ASM154497v2_genomic.fna/markers.fasta)
[2024-01-25 18:27:01,910] [INFO] Task started: Blastn
[2024-01-25 18:27:01,910] [INFO] Running command: blastn -query GCF_001544975.2_ASM154497v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf467a098-519e-4db6-a911-6a02543cd2ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_001544975.2_ASM154497v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:27:03,533] [INFO] Task succeeded: Blastn
[2024-01-25 18:27:03,537] [INFO] Selected 10 target genomes.
[2024-01-25 18:27:03,537] [INFO] Target genome list was writen to GCF_001544975.2_ASM154497v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:27:03,546] [INFO] Task started: fastANI
[2024-01-25 18:27:03,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c368bd2-d6d7-407d-a058-796a7791e0b3/GCF_001544975.2_ASM154497v2_genomic.fna.gz --refList GCF_001544975.2_ASM154497v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001544975.2_ASM154497v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:27:19,076] [INFO] Task succeeded: fastANI
[2024-01-25 18:27:19,082] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:27:19,083] [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
GCF_001544975.2	s__Caballeronia arationis	100.0	2827	2841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.46	99.46	0.88	0.88	2	conclusive
GCF_001544495.1	s__Caballeronia telluris	92.3476	1832	2841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.07	95.07	0.83	0.83	2	-
GCF_001544515.1	s__Caballeronia terrestris	87.0704	1790	2841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544535.1	s__Caballeronia choica	86.8803	1722	2841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544475.1	s__Caballeronia humi	86.6419	1754	2841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.16	95.16	0.85	0.85	2	-
GCF_000698595.1	s__Caballeronia glathei	85.8081	1582	2841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.63	98.92	0.96	0.91	4	-
GCA_902806205.1	s__SEOHO-28 sp902806205	74.7932	102	2841	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012718975.1	s__JAAYBF01 sp012718975	74.7695	129	2841	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Thermoleophilaceae;g__JAAYBF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:27:19,084] [INFO] GTDB search result was written to GCF_001544975.2_ASM154497v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:27:19,084] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:27:19,088] [INFO] DFAST_QC result json was written to GCF_001544975.2_ASM154497v2_genomic.fna/dqc_result.json
[2024-01-25 18:27:19,088] [INFO] DFAST_QC completed!
[2024-01-25 18:27:19,088] [INFO] Total running time: 0h2m13s