[2024-01-24 11:26:28,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference
[2024-01-24 11:26:29,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,556] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,557] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b49e780-573c-43af-997f-5041c834bb71/GCF_002812705.1_ASM281270v1_genomic.fna.gz | prodigal -d GCF_002812705.1_ASM281270v1_genomic.fna/cds.fna -a GCF_002812705.1_ASM281270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:57,447] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:57,447] [INFO] Task started: HMMsearch
[2024-01-24 11:26:57,447] [INFO] Running command: hmmsearch --tblout GCF_002812705.1_ASM281270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference/reference_markers.hmm GCF_002812705.1_ASM281270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:57,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:57,915] [INFO] Found 6/6 markers.
[2024-01-24 11:26:57,967] [INFO] Query marker FASTA was written to GCF_002812705.1_ASM281270v1_genomic.fna/markers.fasta
[2024-01-24 11:26:57,968] [INFO] Task started: Blastn
[2024-01-24 11:26:57,968] [INFO] Running command: blastn -query GCF_002812705.1_ASM281270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference/reference_markers.fasta -out GCF_002812705.1_ASM281270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:58,919] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:58,922] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:58,923] [INFO] Target genome list was writen to GCF_002812705.1_ASM281270v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:58,928] [INFO] Task started: fastANI
[2024-01-24 11:26:58,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b49e780-573c-43af-997f-5041c834bb71/GCF_002812705.1_ASM281270v1_genomic.fna.gz --refList GCF_002812705.1_ASM281270v1_genomic.fna/target_genomes.txt --output GCF_002812705.1_ASM281270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:19,190] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:19,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:19,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:19,203] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:19,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:19,203] [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 spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	100.0	2140	2141	95	conclusive
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	99.9776	2090	2141	95	conclusive
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	88.3628	1720	2141	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	88.332	1731	2141	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.5706	1684	2141	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	87.2621	1583	2141	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	87.2613	1611	2141	95	below_threshold
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	86.3025	1583	2141	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.0184	1457	2141	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.6172	1372	2141	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.5926	813	2141	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.4468	343	2141	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3873	441	2141	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	74.7445	54	2141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:19,204] [INFO] DFAST Taxonomy check result was written to GCF_002812705.1_ASM281270v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:19,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:19,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:19,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference/checkm_data
[2024-01-24 11:27:19,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:19,268] [INFO] Task started: CheckM
[2024-01-24 11:27:19,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002812705.1_ASM281270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002812705.1_ASM281270v1_genomic.fna/checkm_input GCF_002812705.1_ASM281270v1_genomic.fna/checkm_result
[2024-01-24 11:28:38,692] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:38,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:38,718] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:38,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:38,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002812705.1_ASM281270v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:38,720] [INFO] Task started: Blastn
[2024-01-24 11:28:38,720] [INFO] Running command: blastn -query GCF_002812705.1_ASM281270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7726453-8730-407f-9eec-2a0a73b50074/dqc_reference/reference_markers_gtdb.fasta -out GCF_002812705.1_ASM281270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:40,385] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:40,389] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:40,389] [INFO] Target genome list was writen to GCF_002812705.1_ASM281270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:40,399] [INFO] Task started: fastANI
[2024-01-24 11:28:40,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b49e780-573c-43af-997f-5041c834bb71/GCF_002812705.1_ASM281270v1_genomic.fna.gz --refList GCF_002812705.1_ASM281270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002812705.1_ASM281270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:59,561] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:59,576] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:59,577] [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_002812705.1	s__Achromobacter spanius	100.0	2139	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.99	99.98	0.99	0.98	4	conclusive
GCF_003994415.1	s__Achromobacter spanius_C	93.3475	1845	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.60	98.60	0.94	0.94	2	-
GCF_003600685.1	s__Achromobacter spanius_B	88.796	1727	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.56	98.20	0.94	0.92	5	-
GCF_001571245.1	s__Achromobacter piechaudii	88.3709	1719	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.00	98.18	0.96	0.93	8	-
GCF_902859595.1	s__Achromobacter kerstersii	87.5708	1684	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.61	98.61	0.95	0.95	2	-
GCF_014170335.1	s__Achromobacter sp014170335	87.285	1584	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209535.1	s__Achromobacter marplatensis	87.2621	1583	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.15	97.44	0.96	0.90	4	-
GCF_002975275.1	s__Achromobacter sp002975275	86.8199	1583	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859625.1	s__Achromobacter pestifer	86.2905	1585	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428845.1	s__Achromobacter sp001428845	85.5454	1441	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424165.1	s__Massilia sp001424165	76.8789	318	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000263855.1	s__Pseudomonas_E sp000263855	75.8756	183	2141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842085.1	s__CG2-30-64-16 sp002842085	74.832	53	2141	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__CG2-30-64-16;f__CG2-30-64-16;g__CG2-30-64-16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:59,578] [INFO] GTDB search result was written to GCF_002812705.1_ASM281270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:59,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:59,582] [INFO] DFAST_QC result json was written to GCF_002812705.1_ASM281270v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:59,582] [INFO] DFAST_QC completed!
[2024-01-24 11:28:59,582] [INFO] Total running time: 0h2m31s