[2024-01-24 12:29:52,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference
[2024-01-24 12:29:54,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:54,069] [INFO] Task started: Prodigal
[2024-01-24 12:29:54,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg9272900c-48d1-42b5-89aa-38fb4248caa7/GCF_008801925.2_ASM880192v2_genomic.fna.gz | prodigal -d GCF_008801925.2_ASM880192v2_genomic.fna/cds.fna -a GCF_008801925.2_ASM880192v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:26,315] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:26,316] [INFO] Task started: HMMsearch
[2024-01-24 12:30:26,316] [INFO] Running command: hmmsearch --tblout GCF_008801925.2_ASM880192v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference/reference_markers.hmm GCF_008801925.2_ASM880192v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:26,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:26,688] [INFO] Found 6/6 markers.
[2024-01-24 12:30:26,755] [INFO] Query marker FASTA was written to GCF_008801925.2_ASM880192v2_genomic.fna/markers.fasta
[2024-01-24 12:30:26,755] [INFO] Task started: Blastn
[2024-01-24 12:30:26,756] [INFO] Running command: blastn -query GCF_008801925.2_ASM880192v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference/reference_markers.fasta -out GCF_008801925.2_ASM880192v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:27,844] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:27,851] [INFO] Selected 21 target genomes.
[2024-01-24 12:30:27,852] [INFO] Target genome list was writen to GCF_008801925.2_ASM880192v2_genomic.fna/target_genomes.txt
[2024-01-24 12:30:27,870] [INFO] Task started: fastANI
[2024-01-24 12:30:27,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg9272900c-48d1-42b5-89aa-38fb4248caa7/GCF_008801925.2_ASM880192v2_genomic.fna.gz --refList GCF_008801925.2_ASM880192v2_genomic.fna/target_genomes.txt --output GCF_008801925.2_ASM880192v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:00,755] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:00,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:00,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:00,779] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:00,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:00,780] [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
Cupriavidus basilensis	strain=DSM 11853	GCA_008801925.2	68895	68895	suspected-type	True	100.0	2975	2977	95	conclusive
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	83.8394	1343	2977	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	83.3378	1281	2977	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	83.3007	1273	2977	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	83.2625	1377	2977	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	83.2198	1285	2977	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	83.1599	1293	2977	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	83.1167	1266	2977	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	82.8449	1112	2977	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	82.812	1450	2977	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	82.4641	1086	2977	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	82.4373	1096	2977	95	below_threshold
Cupriavidus campinensis	strain=LMG 19282	GCA_905397395.1	151783	151783	type	True	82.4104	1152	2977	95	below_threshold
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	82.1835	1121	2977	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.0969	1293	2977	95	below_threshold
Cupriavidus pauculus	strain=FDAARGOS_1472	GCA_019931045.1	82633	82633	type	True	81.4447	1154	2977	95	below_threshold
Cupriavidus pauculus	strain=CCUG 12507	GCA_008801835.1	82633	82633	type	True	81.2736	1143	2977	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.0117	712	2977	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.9308	520	2977	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	77.8759	698	2977	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	77.5799	524	2977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:00,782] [INFO] DFAST Taxonomy check result was written to GCF_008801925.2_ASM880192v2_genomic.fna/tc_result.tsv
[2024-01-24 12:31:00,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:00,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:00,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference/checkm_data
[2024-01-24 12:31:00,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:00,874] [INFO] Task started: CheckM
[2024-01-24 12:31:00,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801925.2_ASM880192v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801925.2_ASM880192v2_genomic.fna/checkm_input GCF_008801925.2_ASM880192v2_genomic.fna/checkm_result
[2024-01-24 12:32:34,564] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:34,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:34,587] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:34,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:34,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801925.2_ASM880192v2_genomic.fna/markers.fasta)
[2024-01-24 12:32:34,588] [INFO] Task started: Blastn
[2024-01-24 12:32:34,588] [INFO] Running command: blastn -query GCF_008801925.2_ASM880192v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg28be3423-6a57-464c-8d2b-44c7263b28fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801925.2_ASM880192v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:36,747] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:36,749] [INFO] Selected 12 target genomes.
[2024-01-24 12:32:36,750] [INFO] Target genome list was writen to GCF_008801925.2_ASM880192v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:36,768] [INFO] Task started: fastANI
[2024-01-24 12:32:36,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg9272900c-48d1-42b5-89aa-38fb4248caa7/GCF_008801925.2_ASM880192v2_genomic.fna.gz --refList GCF_008801925.2_ASM880192v2_genomic.fna/target_genomes_gtdb.txt --output GCF_008801925.2_ASM880192v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:00,746] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:00,763] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:00,763] [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_008801925.2	s__Cupriavidus basilensis	100.0	2976	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.09	95.23	0.79	0.75	4	conclusive
GCF_000243095.1	s__Cupriavidus basilensis_D	92.0118	1967	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955785.1	s__Cupriavidus sp000955785	88.1409	1882	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.82	95.82	0.77	0.77	2	-
GCF_000876015.1	s__Cupriavidus basilensis_B	86.188	1603	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCF_001598055.1	s__Cupriavidus nantongensis	83.8217	1345	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_900249755.1	s__Cupriavidus taiwanensis_D	83.6658	1264	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.80	98.80	0.92	0.92	2	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	83.3311	1282	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_000069785.1	s__Cupriavidus taiwanensis	83.2647	1279	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.86	98.78	0.92	0.91	9	-
GCA_000471925.1	s__Cupriavidus pickettii_A	83.1208	1366	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744095.1	s__Cupriavidus necator_A	83.0561	1445	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812465.1	s__Cupriavidus sp000812465	83.0523	1334	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397395.1	s__Cupriavidus campinensis	82.3993	1152	2977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.28	95.05	0.89	0.86	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:00,765] [INFO] GTDB search result was written to GCF_008801925.2_ASM880192v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:00,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:00,769] [INFO] DFAST_QC result json was written to GCF_008801925.2_ASM880192v2_genomic.fna/dqc_result.json
[2024-01-24 12:33:00,770] [INFO] DFAST_QC completed!
[2024-01-24 12:33:00,770] [INFO] Total running time: 0h3m8s