[2024-01-24 12:31:04,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,720] [INFO] DQC Reference Directory: /var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference
[2024-01-24 12:31:06,051] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:06,052] [INFO] Task started: Prodigal
[2024-01-24 12:31:06,052] [INFO] Running command: gunzip -c /var/lib/cwl/stg554d536c-996c-4c3f-9622-8213b4798f9f/GCF_905397435.1_LMG_26411_genomic.fna.gz | prodigal -d GCF_905397435.1_LMG_26411_genomic.fna/cds.fna -a GCF_905397435.1_LMG_26411_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:36,968] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:36,968] [INFO] Task started: HMMsearch
[2024-01-24 12:31:36,968] [INFO] Running command: hmmsearch --tblout GCF_905397435.1_LMG_26411_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference/reference_markers.hmm GCF_905397435.1_LMG_26411_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:37,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:37,406] [INFO] Found 6/6 markers.
[2024-01-24 12:31:37,482] [INFO] Query marker FASTA was written to GCF_905397435.1_LMG_26411_genomic.fna/markers.fasta
[2024-01-24 12:31:37,483] [INFO] Task started: Blastn
[2024-01-24 12:31:37,483] [INFO] Running command: blastn -query GCF_905397435.1_LMG_26411_genomic.fna/markers.fasta -db /var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference/reference_markers.fasta -out GCF_905397435.1_LMG_26411_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:38,471] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:38,474] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:38,475] [INFO] Target genome list was writen to GCF_905397435.1_LMG_26411_genomic.fna/target_genomes.txt
[2024-01-24 12:31:38,488] [INFO] Task started: fastANI
[2024-01-24 12:31:38,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg554d536c-996c-4c3f-9622-8213b4798f9f/GCF_905397435.1_LMG_26411_genomic.fna.gz --refList GCF_905397435.1_LMG_26411_genomic.fna/target_genomes.txt --output GCF_905397435.1_LMG_26411_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:01,971] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:01,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:01,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:01,989] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:01,989] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:01,989] [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 numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	100.0	2926	2935	95	conclusive
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	84.8122	1394	2935	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	84.7136	1348	2935	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	84.6686	1365	2935	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	84.6026	1503	2935	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	84.5946	1396	2935	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	84.5909	1476	2935	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	84.4681	1541	2935	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	78.3429	484	2935	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.3248	706	2935	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	77.9677	578	2935	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.756	573	2935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,990] [INFO] DFAST Taxonomy check result was written to GCF_905397435.1_LMG_26411_genomic.fna/tc_result.tsv
[2024-01-24 12:32:01,991] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:01,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:01,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference/checkm_data
[2024-01-24 12:32:01,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:02,073] [INFO] Task started: CheckM
[2024-01-24 12:32:02,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_905397435.1_LMG_26411_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_905397435.1_LMG_26411_genomic.fna/checkm_input GCF_905397435.1_LMG_26411_genomic.fna/checkm_result
[2024-01-24 12:33:32,169] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:32,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:32,197] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:32,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:32,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_905397435.1_LMG_26411_genomic.fna/markers.fasta)
[2024-01-24 12:33:32,199] [INFO] Task started: Blastn
[2024-01-24 12:33:32,199] [INFO] Running command: blastn -query GCF_905397435.1_LMG_26411_genomic.fna/markers.fasta -db /var/lib/cwl/stge0f73f8e-4e38-484d-9b74-565e92f7a0cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_905397435.1_LMG_26411_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:33,786] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:33,790] [INFO] Selected 18 target genomes.
[2024-01-24 12:33:33,790] [INFO] Target genome list was writen to GCF_905397435.1_LMG_26411_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:33,811] [INFO] Task started: fastANI
[2024-01-24 12:33:33,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg554d536c-996c-4c3f-9622-8213b4798f9f/GCF_905397435.1_LMG_26411_genomic.fna.gz --refList GCF_905397435.1_LMG_26411_genomic.fna/target_genomes_gtdb.txt --output GCF_905397435.1_LMG_26411_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:05,087] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:05,105] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:34:05,106] [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_905397435.1	s__Cupriavidus numazuensis	100.0	2926	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000203875.1	s__Cupriavidus pinatubonensis	93.3498	1973	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.67	99.34	0.94	0.87	3	-
GCA_001725945.1	s__Cupriavidus sp001725945	88.5105	1657	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397275.1	s__Cupriavidus yeoncheonensis	88.1741	1705	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	84.8561	1387	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCF_017814975.1	s__Cupriavidus sp017814975	84.6448	1614	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894385.1	s__Cupriavidus oxalaticus	84.6348	1497	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.73	98.93	0.98	0.92	5	-
GCF_900250075.1	s__Cupriavidus taiwanensis_C	84.5972	1422	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.42	95.79	0.88	0.85	6	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	84.5748	1399	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_000426345.1	s__Cupriavidus sp000426345	84.4379	1496	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.93	98.88	0.87	0.86	3	-
GCF_000219215.1	s__Cupriavidus necator	84.4202	1574	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.10	95.22	0.79	0.76	13	-
GCA_000471925.1	s__Cupriavidus pickettii_A	84.3895	1567	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141915.1	s__Cupriavidus necator_B	84.3784	1409	2935	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	84.3677	1447	2935	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	84.291	1605	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	77.6905	406	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106025.1	s__Methylococcus sp016106025	75.7394	80	2935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:05,107] [INFO] GTDB search result was written to GCF_905397435.1_LMG_26411_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:05,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:05,113] [INFO] DFAST_QC result json was written to GCF_905397435.1_LMG_26411_genomic.fna/dqc_result.json
[2024-01-24 12:34:05,114] [INFO] DFAST_QC completed!
[2024-01-24 12:34:05,114] [INFO] Total running time: 0h3m0s