[2024-01-25 18:15:35,611] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference
[2024-01-25 18:15:36,776] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,777] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,777] [INFO] Running command: gunzip -c /var/lib/cwl/stgc639b6ec-4051-4218-bb00-76e6ccde325a/GCF_902859625.1_LMG_3431_genomic.fna.gz | prodigal -d GCF_902859625.1_LMG_3431_genomic.fna/cds.fna -a GCF_902859625.1_LMG_3431_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:01,020] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:01,020] [INFO] Task started: HMMsearch
[2024-01-25 18:16:01,021] [INFO] Running command: hmmsearch --tblout GCF_902859625.1_LMG_3431_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference/reference_markers.hmm GCF_902859625.1_LMG_3431_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:01,323] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:01,325] [INFO] Found 6/6 markers.
[2024-01-25 18:16:01,378] [INFO] Query marker FASTA was written to GCF_902859625.1_LMG_3431_genomic.fna/markers.fasta
[2024-01-25 18:16:01,378] [INFO] Task started: Blastn
[2024-01-25 18:16:01,378] [INFO] Running command: blastn -query GCF_902859625.1_LMG_3431_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference/reference_markers.fasta -out GCF_902859625.1_LMG_3431_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:02,256] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:02,259] [INFO] Selected 12 target genomes.
[2024-01-25 18:16:02,259] [INFO] Target genome list was writen to GCF_902859625.1_LMG_3431_genomic.fna/target_genomes.txt
[2024-01-25 18:16:02,277] [INFO] Task started: fastANI
[2024-01-25 18:16:02,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgc639b6ec-4051-4218-bb00-76e6ccde325a/GCF_902859625.1_LMG_3431_genomic.fna.gz --refList GCF_902859625.1_LMG_3431_genomic.fna/target_genomes.txt --output GCF_902859625.1_LMG_3431_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:20,285] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:20,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:20,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:20,300] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:20,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:20,301] [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 pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	100.0	2292	2293	95	conclusive
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	88.4942	1794	2293	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	88.48	1793	2293	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	88.4545	1822	2293	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	86.7873	1680	2293	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	86.2575	1599	2293	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	86.2074	1578	2293	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.4505	1496	2293	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	84.3404	1526	2293	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.0021	797	2293	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.0819	174	2293	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	76.7049	272	2293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:20,302] [INFO] DFAST Taxonomy check result was written to GCF_902859625.1_LMG_3431_genomic.fna/tc_result.tsv
[2024-01-25 18:16:20,303] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:20,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:20,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference/checkm_data
[2024-01-25 18:16:20,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:20,371] [INFO] Task started: CheckM
[2024-01-25 18:16:20,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859625.1_LMG_3431_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859625.1_LMG_3431_genomic.fna/checkm_input GCF_902859625.1_LMG_3431_genomic.fna/checkm_result
[2024-01-25 18:17:39,541] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:39,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:39,580] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:39,580] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:39,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859625.1_LMG_3431_genomic.fna/markers.fasta)
[2024-01-25 18:17:39,581] [INFO] Task started: Blastn
[2024-01-25 18:17:39,581] [INFO] Running command: blastn -query GCF_902859625.1_LMG_3431_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a7a5c6c-edd9-45cb-b476-ed7e100a4ab4/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859625.1_LMG_3431_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:41,363] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:41,368] [INFO] Selected 10 target genomes.
[2024-01-25 18:17:41,368] [INFO] Target genome list was writen to GCF_902859625.1_LMG_3431_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:41,384] [INFO] Task started: fastANI
[2024-01-25 18:17:41,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgc639b6ec-4051-4218-bb00-76e6ccde325a/GCF_902859625.1_LMG_3431_genomic.fna.gz --refList GCF_902859625.1_LMG_3431_genomic.fna/target_genomes_gtdb.txt --output GCF_902859625.1_LMG_3431_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:58,757] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:58,764] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:58,765] [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_902859625.1	s__Achromobacter pestifer	100.0	2292	2293	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_014170335.1	s__Achromobacter sp014170335	88.6364	1835	2293	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	88.4723	1794	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.15	97.44	0.96	0.90	4	-
GCF_012928505.1	s__Achromobacter sp012928505	88.2884	1785	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975275.1	s__Achromobacter sp002975275	87.8025	1754	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859595.1	s__Achromobacter kerstersii	86.7946	1679	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.61	98.61	0.95	0.95	2	-
GCF_002812705.1	s__Achromobacter spanius	86.2521	1600	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.99	99.98	0.99	0.98	4	-
GCF_001571245.1	s__Achromobacter piechaudii	86.0033	1590	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.00	98.18	0.96	0.93	8	-
GCF_003994415.1	s__Achromobacter spanius_C	85.9989	1534	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.60	98.60	0.94	0.94	2	-
GCF_013116765.2	s__Achromobacter deleyi_A	85.9365	1565	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:58,766] [INFO] GTDB search result was written to GCF_902859625.1_LMG_3431_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:58,766] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:58,769] [INFO] DFAST_QC result json was written to GCF_902859625.1_LMG_3431_genomic.fna/dqc_result.json
[2024-01-25 18:17:58,769] [INFO] DFAST_QC completed!
[2024-01-25 18:17:58,769] [INFO] Total running time: 0h2m23s