[2024-01-24 13:09:28,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:28,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:28,952] [INFO] DQC Reference Directory: /var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference
[2024-01-24 13:09:30,170] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,171] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,171] [INFO] Running command: gunzip -c /var/lib/cwl/stgae19821c-8093-439c-a974-bc3812ce403c/GCF_900496975.1_LMG_30378_genomic.fna.gz | prodigal -d GCF_900496975.1_LMG_30378_genomic.fna/cds.fna -a GCF_900496975.1_LMG_30378_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:50,358] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:50,359] [INFO] Task started: HMMsearch
[2024-01-24 13:09:50,359] [INFO] Running command: hmmsearch --tblout GCF_900496975.1_LMG_30378_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference/reference_markers.hmm GCF_900496975.1_LMG_30378_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:50,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:50,774] [INFO] Found 6/6 markers.
[2024-01-24 13:09:50,831] [INFO] Query marker FASTA was written to GCF_900496975.1_LMG_30378_genomic.fna/markers.fasta
[2024-01-24 13:09:50,832] [INFO] Task started: Blastn
[2024-01-24 13:09:50,832] [INFO] Running command: blastn -query GCF_900496975.1_LMG_30378_genomic.fna/markers.fasta -db /var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference/reference_markers.fasta -out GCF_900496975.1_LMG_30378_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:51,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:51,934] [INFO] Selected 15 target genomes.
[2024-01-24 13:09:51,935] [INFO] Target genome list was writen to GCF_900496975.1_LMG_30378_genomic.fna/target_genomes.txt
[2024-01-24 13:09:51,941] [INFO] Task started: fastANI
[2024-01-24 13:09:51,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgae19821c-8093-439c-a974-bc3812ce403c/GCF_900496975.1_LMG_30378_genomic.fna.gz --refList GCF_900496975.1_LMG_30378_genomic.fna/target_genomes.txt --output GCF_900496975.1_LMG_30378_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:17,419] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:17,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:17,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:17,438] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:17,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:17,438] [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
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	100.0	2216	2219	95	conclusive
Achromobacter denitrificans	strain=NCTC8582	GCA_900444675.1	32002	32002	type	True	91.1786	1707	2219	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	91.1537	1710	2219	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	91.142	1741	2219	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	91.1319	1722	2219	95	below_threshold
Achromobacter agilis	strain=LMG 3411	GCA_900496965.1	1353888	1353888	type	True	90.8908	1661	2219	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	87.0487	1529	2219	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	86.7562	1396	2219	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	86.593	1436	2219	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	86.5667	1450	2219	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	86.4832	1473	2219	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	86.4052	1435	2219	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.5461	927	2219	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.9128	363	2219	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.5235	507	2219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:17,440] [INFO] DFAST Taxonomy check result was written to GCF_900496975.1_LMG_30378_genomic.fna/tc_result.tsv
[2024-01-24 13:10:17,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:17,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:17,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference/checkm_data
[2024-01-24 13:10:17,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:17,515] [INFO] Task started: CheckM
[2024-01-24 13:10:17,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900496975.1_LMG_30378_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900496975.1_LMG_30378_genomic.fna/checkm_input GCF_900496975.1_LMG_30378_genomic.fna/checkm_result
[2024-01-24 13:11:17,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:17,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:17,857] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:17,857] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:17,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900496975.1_LMG_30378_genomic.fna/markers.fasta)
[2024-01-24 13:11:17,858] [INFO] Task started: Blastn
[2024-01-24 13:11:17,859] [INFO] Running command: blastn -query GCF_900496975.1_LMG_30378_genomic.fna/markers.fasta -db /var/lib/cwl/stgd98779ad-31be-4488-bc50-0640e407171e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900496975.1_LMG_30378_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:20,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:20,011] [INFO] Selected 10 target genomes.
[2024-01-24 13:11:20,011] [INFO] Target genome list was writen to GCF_900496975.1_LMG_30378_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:20,027] [INFO] Task started: fastANI
[2024-01-24 13:11:20,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgae19821c-8093-439c-a974-bc3812ce403c/GCF_900496975.1_LMG_30378_genomic.fna.gz --refList GCF_900496975.1_LMG_30378_genomic.fna/target_genomes_gtdb.txt --output GCF_900496975.1_LMG_30378_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:38,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:38,154] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:38,154] [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_900496975.1	s__Achromobacter veterisilvae	100.0	2216	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001571365.1	s__Achromobacter denitrificans	91.1302	1722	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_900496965.1	s__Achromobacter agilis	90.9006	1660	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757485.1	s__Achromobacter sp000757485	90.5571	1647	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	89.236	1475	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_903652925.1	s__Achromobacter anxifer	88.5012	1539	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	-
GCF_902859645.1	s__Achromobacter insuavis	86.7565	1396	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_014170335.1	s__Achromobacter sp014170335	86.6282	1462	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016127315.1	s__Achromobacter insuavis_A	86.6178	1463	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_001457475.1	s__Achromobacter xylosoxidans	86.4685	1475	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:38,156] [INFO] GTDB search result was written to GCF_900496975.1_LMG_30378_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:38,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:38,160] [INFO] DFAST_QC result json was written to GCF_900496975.1_LMG_30378_genomic.fna/dqc_result.json
[2024-01-24 13:11:38,160] [INFO] DFAST_QC completed!
[2024-01-24 13:11:38,160] [INFO] Total running time: 0h2m9s