[2024-01-24 12:54:39,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference
[2024-01-24 12:54:40,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:40,987] [INFO] Task started: Prodigal
[2024-01-24 12:54:40,987] [INFO] Running command: gunzip -c /var/lib/cwl/stgf582c13e-807e-469d-8efa-e04647214909/GCF_001017775.3_ASM101777v3_genomic.fna.gz | prodigal -d GCF_001017775.3_ASM101777v3_genomic.fna/cds.fna -a GCF_001017775.3_ASM101777v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:58,288] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:58,289] [INFO] Task started: HMMsearch
[2024-01-24 12:54:58,289] [INFO] Running command: hmmsearch --tblout GCF_001017775.3_ASM101777v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference/reference_markers.hmm GCF_001017775.3_ASM101777v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:58,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:58,623] [INFO] Found 6/6 markers.
[2024-01-24 12:54:58,662] [INFO] Query marker FASTA was written to GCF_001017775.3_ASM101777v3_genomic.fna/markers.fasta
[2024-01-24 12:54:58,663] [INFO] Task started: Blastn
[2024-01-24 12:54:58,663] [INFO] Running command: blastn -query GCF_001017775.3_ASM101777v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference/reference_markers.fasta -out GCF_001017775.3_ASM101777v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:59,635] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:59,638] [INFO] Selected 22 target genomes.
[2024-01-24 12:54:59,639] [INFO] Target genome list was writen to GCF_001017775.3_ASM101777v3_genomic.fna/target_genomes.txt
[2024-01-24 12:54:59,648] [INFO] Task started: fastANI
[2024-01-24 12:54:59,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgf582c13e-807e-469d-8efa-e04647214909/GCF_001017775.3_ASM101777v3_genomic.fna.gz --refList GCF_001017775.3_ASM101777v3_genomic.fna/target_genomes.txt --output GCF_001017775.3_ASM101777v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:22,925] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:22,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:22,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:22,948] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:55:22,949] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:22,949] [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
Pandoraea thiooxydans	strain=DSM 25325	GCA_001017775.3	445709	445709	type	True	100.0	1488	1488	95	conclusive
Pandoraea thiooxydans	strain=ATSB16	GCA_001931675.1	445709	445709	type	True	99.9999	1487	1488	95	conclusive
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	78.6809	462	1488	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	78.6566	461	1488	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	78.5248	516	1488	95	below_threshold
Pandoraea pnomenusa	strain=NCTC13160	GCA_900454355.1	93220	93220	type	True	78.3426	495	1488	95	below_threshold
Pandoraea terrigena	strain=LMG 31013	GCA_902459705.1	2508292	2508292	type	True	78.3099	451	1488	95	below_threshold
Pandoraea pnomenusa	strain=DSM 16536	GCA_000767615.3	93220	93220	type	True	78.2737	492	1488	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	78.2386	424	1488	95	below_threshold
Pandoraea morbifera	strain=LMG 31116	GCA_902459575.1	2508300	2508300	type	True	78.1795	471	1488	95	below_threshold
Pandoraea sputorum	strain=DSM 21091	GCA_000814845.2	93222	93222	type	True	78.1691	441	1488	95	below_threshold
Pandoraea norimbergensis	strain=DSM 11628	GCA_001465545.3	93219	93219	type	True	78.1291	460	1488	95	below_threshold
Pandoraea iniqua	strain=LMG 31009	GCA_902459685.1	2508288	2508288	type	True	77.9932	458	1488	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	77.9898	392	1488	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	77.8887	546	1488	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	77.8475	526	1488	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	77.733	468	1488	95	below_threshold
Burkholderia pseudomultivorans		GCA_902499075.1	1207504	1207504	suspected-type	True	77.6911	476	1488	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	77.4945	469	1488	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	77.4323	433	1488	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	77.43	364	1488	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	77.4249	307	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:22,951] [INFO] DFAST Taxonomy check result was written to GCF_001017775.3_ASM101777v3_genomic.fna/tc_result.tsv
[2024-01-24 12:55:22,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:22,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:22,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference/checkm_data
[2024-01-24 12:55:22,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:22,995] [INFO] Task started: CheckM
[2024-01-24 12:55:22,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001017775.3_ASM101777v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001017775.3_ASM101777v3_genomic.fna/checkm_input GCF_001017775.3_ASM101777v3_genomic.fna/checkm_result
[2024-01-24 12:56:13,300] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:13,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:13,324] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:13,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:13,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001017775.3_ASM101777v3_genomic.fna/markers.fasta)
[2024-01-24 12:56:13,326] [INFO] Task started: Blastn
[2024-01-24 12:56:13,326] [INFO] Running command: blastn -query GCF_001017775.3_ASM101777v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgde16818f-ce14-4193-8744-d9924219682a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001017775.3_ASM101777v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:15,127] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:15,132] [INFO] Selected 15 target genomes.
[2024-01-24 12:56:15,132] [INFO] Target genome list was writen to GCF_001017775.3_ASM101777v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:15,143] [INFO] Task started: fastANI
[2024-01-24 12:56:15,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgf582c13e-807e-469d-8efa-e04647214909/GCF_001017775.3_ASM101777v3_genomic.fna.gz --refList GCF_001017775.3_ASM101777v3_genomic.fna/target_genomes_gtdb.txt --output GCF_001017775.3_ASM101777v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:31,007] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:31,032] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:31,032] [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_001931675.1	s__Pandoraea thiooxydans	99.9999	1487	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018971155.1	s__Pandoraea sp018971155	93.2054	890	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297875.1	s__Pandoraea sp004297875	91.7086	1240	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000815105.2	s__Pandoraea pulmonicola	78.7408	460	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902459585.1	s__Pandoraea nosoerga	78.5328	515	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.66	99.29	0.94	0.91	4	-
GCF_902459695.1	s__Pandoraea terrae	78.5305	484	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459705.1	s__Pandoraea terrigena	78.3448	447	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767615.3	s__Pandoraea pnomenusa	78.2655	493	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.00	95.12	0.95	0.92	14	-
GCF_002179965.1	s__Pandoraea sp002179965	78.1336	436	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	98.74	98.74	0.95	0.95	2	-
GCF_001465545.3	s__Pandoraea norimbergensis	78.0885	460	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251695.1	s__Ralstonia solanacearum	77.968	388	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.27	95.49	0.87	0.78	131	-
GCF_011752995.1	s__Paraburkholderia sp011752995	77.9414	433	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_000959725.1	s__Burkholderia gladioli	77.9182	540	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.34	97.08	0.90	0.82	265	-
GCF_902499075.1	s__Burkholderia pseudomultivorans	77.7166	470	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.22	95.54	0.83	0.81	13	-
GCF_001544475.1	s__Caballeronia humi	77.3153	357	1488	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	95.16	95.16	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:31,034] [INFO] GTDB search result was written to GCF_001017775.3_ASM101777v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:31,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:31,042] [INFO] DFAST_QC result json was written to GCF_001017775.3_ASM101777v3_genomic.fna/dqc_result.json
[2024-01-24 12:56:31,042] [INFO] DFAST_QC completed!
[2024-01-24 12:56:31,042] [INFO] Total running time: 0h1m51s