[2024-01-24 11:43:41,902] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference
[2024-01-24 11:43:43,228] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,229] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,229] [INFO] Running command: gunzip -c /var/lib/cwl/stg781a7ae7-313b-4782-80e2-9f89855faa96/GCF_902859605.1_LMG_5911_genomic.fna.gz | prodigal -d GCF_902859605.1_LMG_5911_genomic.fna/cds.fna -a GCF_902859605.1_LMG_5911_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:05,235] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:05,235] [INFO] Task started: HMMsearch
[2024-01-24 11:44:05,235] [INFO] Running command: hmmsearch --tblout GCF_902859605.1_LMG_5911_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference/reference_markers.hmm GCF_902859605.1_LMG_5911_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,789] [INFO] Found 6/6 markers.
[2024-01-24 11:44:05,859] [INFO] Query marker FASTA was written to GCF_902859605.1_LMG_5911_genomic.fna/markers.fasta
[2024-01-24 11:44:05,860] [INFO] Task started: Blastn
[2024-01-24 11:44:05,860] [INFO] Running command: blastn -query GCF_902859605.1_LMG_5911_genomic.fna/markers.fasta -db /var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference/reference_markers.fasta -out GCF_902859605.1_LMG_5911_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:06,903] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:06,907] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:06,907] [INFO] Target genome list was writen to GCF_902859605.1_LMG_5911_genomic.fna/target_genomes.txt
[2024-01-24 11:44:06,913] [INFO] Task started: fastANI
[2024-01-24 11:44:06,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg781a7ae7-313b-4782-80e2-9f89855faa96/GCF_902859605.1_LMG_5911_genomic.fna.gz --refList GCF_902859605.1_LMG_5911_genomic.fna/target_genomes.txt --output GCF_902859605.1_LMG_5911_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:27,230] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:27,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:27,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:27,247] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:27,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:27,247] [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=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	100.0	2085	2090	95	conclusive
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	99.9987	2090	2090	95	conclusive
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	88.3953	1706	2090	95	below_threshold
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	88.3418	1697	2090	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.5525	1656	2090	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	87.2979	1591	2090	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	87.2668	1581	2090	95	below_threshold
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	86.3237	1562	2090	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.0072	1449	2090	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.5168	1359	2090	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.4922	837	2090	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.428	344	2090	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.4209	413	2090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:27,249] [INFO] DFAST Taxonomy check result was written to GCF_902859605.1_LMG_5911_genomic.fna/tc_result.tsv
[2024-01-24 11:44:27,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:27,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:27,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference/checkm_data
[2024-01-24 11:44:27,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:27,310] [INFO] Task started: CheckM
[2024-01-24 11:44:27,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859605.1_LMG_5911_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859605.1_LMG_5911_genomic.fna/checkm_input GCF_902859605.1_LMG_5911_genomic.fna/checkm_result
[2024-01-24 11:45:30,462] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:30,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:30,487] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:30,487] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:30,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859605.1_LMG_5911_genomic.fna/markers.fasta)
[2024-01-24 11:45:30,488] [INFO] Task started: Blastn
[2024-01-24 11:45:30,488] [INFO] Running command: blastn -query GCF_902859605.1_LMG_5911_genomic.fna/markers.fasta -db /var/lib/cwl/stg71bcbd9c-3930-4430-b220-9f9a3a2636ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859605.1_LMG_5911_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:32,127] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:32,132] [INFO] Selected 13 target genomes.
[2024-01-24 11:45:32,132] [INFO] Target genome list was writen to GCF_902859605.1_LMG_5911_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:32,141] [INFO] Task started: fastANI
[2024-01-24 11:45:32,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg781a7ae7-313b-4782-80e2-9f89855faa96/GCF_902859605.1_LMG_5911_genomic.fna.gz --refList GCF_902859605.1_LMG_5911_genomic.fna/target_genomes_gtdb.txt --output GCF_902859605.1_LMG_5911_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:50,927] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:50,948] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:50,949] [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	99.9987	2090	2090	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	93.389	1795	2090	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	88.7649	1705	2090	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	88.35	1696	2090	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	87.5577	1655	2090	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	87.3235	1566	2090	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	87.2346	1585	2090	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	86.8791	1578	2090	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	86.3007	1567	2090	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	85.5718	1431	2090	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	76.688	322	2090	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	75.7692	180	2090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:50,951] [INFO] GTDB search result was written to GCF_902859605.1_LMG_5911_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:50,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:50,955] [INFO] DFAST_QC result json was written to GCF_902859605.1_LMG_5911_genomic.fna/dqc_result.json
[2024-01-24 11:45:50,955] [INFO] DFAST_QC completed!
[2024-01-24 11:45:50,955] [INFO] Total running time: 0h2m9s